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
ADAMTS17	170691	broad.mit.edu	37	15	100636613	100636613	+	Silent	SNP	G	G	A	rs141443664		TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr15:100636613G>A	ENST00000268070.4	-	15	2190	c.2085C>T	c.(2083-2085)gaC>gaT	p.D695D		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	695	Cys-rich.				proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		AGGTCTTGCCGTCCCCGCTGC	0.592		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0								G		0,4406		0,0,2203	94	101	99		2085	-3.6	0.9	15	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADAMTS17	NM_139057.2		0,1,6502	AA,AG,GG	NA	0.0116,0.0,0.0077		695/1096	100636613	1,13005	2203	4300	6503	SO:0001819	synonymous_variant			AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470	170691	170691		ADAM metallopeptidases with thrombospondin type 1 motif	17109	protein-coding gene	gene with protein product		607511	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17		NA	11867212	Standard	NM_139057	NM_139057	NA	Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.2085C>T	15.37:g.100636613G>A		NA	Q2I7G4|Q6ZN75	37	CCDS10383.1																																																																																			ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313595.1		-	ENST00000268070.4	Silent	SNP	15 : 100636613 - 100636613 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	539	6
AGO2	27161	broad.mit.edu	37	8	141554316	141554316	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr8:141554316G>A	ENST00000220592.5	-	14	1947	c.1835C>T	c.(1834-1836)gCc>gTc	p.A612V	AGO2_ENST00000519980.1_Missense_Mutation_p.A612V	NM_012154.3	NP_036286.2			argonaute RISC catalytic component 2	NA											NA						ACTCACGGCGGCAATGGAGGG	0.632		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													103	114	110			NA	NA	8		NA											NA				141554316		2203	4300	6503	SO:0001583	missense			AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908	27161	27161		Argonaute/PIWI family	3263	protein-coding gene	gene with protein product	argonaute 2	606229	eukaryotic translation initiation factor 2C, 2	EIF2C2	NA	10534406, 12906857	Standard		NM_012154	NA	Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.1835C>T	8.37:g.141554316G>A	ENSP00000220592:p.Ala612Val	NA		37	CCDS6380.1	.	.	.	.	.	.	.	.	.	.	G	30	5.051705	0.93793	.	.	ENSG00000123908	ENST00000220592;ENST00000519980	T;T	0.29397	1.57;1.57	5.35	5.35	0.76521	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.49218	0.1544	L	0.52126	1.63	0.80722	D	1	P;P	0.41569	0.742;0.755	P;P	0.56612	0.7;0.802	T	0.36237	-0.9756	10	0.52906	T	0.07	-4.8173	19.4318	0.94772	0.0:0.0:1.0:0.0	.	612;612	Q9UKV8-2;Q9UKV8	.;AGO2_HUMAN	V	612	ENSP00000220592:A612V;ENSP00000430176:A612V	ENSP00000220592:A612V	A	-	2	0	EIF2C2	141623498	1.000000	0.71417	0.180000	0.23079	0.810000	0.45777	9.744000	0.98853	2.664000	0.90586	0.650000	0.86243	GCC	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377866.4		-	ENST00000220592.5	Missense_Mutation	SNP	8 : 141554316 - 141554316 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	966	6
ANAPC1	64682	broad.mit.edu	37	2	112608394	112608394	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	T	T	-	-	T	T	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr2:112608394T>C	ENST00000341068.3	-	14	2381	c.1609A>G	c.(1609-1611)Act>Gct	p.T537A		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	537					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm		p.T537A(5)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						GGCTTTGGAGTACTAACGCCA	0.433		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				5	Substitution - Missense(5)	lung(3)|kidney(1)|endometrium(1)											109	106	107			NA	NA	2		NA											NA				112608394		2203	4300	6503	SO:0001583	missense			AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107	64682	64682		Anaphase promoting complex subunits	19988	protein-coding gene	gene with protein product		608473			NA	11179667	Standard	NM_022662	NM_022662	NA	Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.1609A>G	2.37:g.112608394T>C	ENSP00000339109:p.Thr537Ala	NA	Q2M3H8|Q9BSE6|Q9H8D0	37	CCDS2093.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.716|4.716	0.133071|0.133071	0.09032|0.09032	.|.	.|.	ENSG00000153107|ENSG00000153107	ENST00000341068|ENST00000427997	.|.	.|.	.|.	4.57|4.57	3.37|3.37	0.38596|0.38596	.|.	0.273018|.	0.23039|.	U|.	0.052629|.	T|T	0.55305|0.55305	0.1912|0.1912	L|L	0.45352|0.45352	1.415|1.415	0.37887|0.37887	D|D	0.930579|0.930579	B|.	0.14438|.	0.01|.	B|.	0.18263|.	0.021|.	T|T	0.53535|0.53535	-0.8425|-0.8425	9|5	0.08837|.	T|.	0.75|.	-8.0757|-8.0757	10.3103|10.3103	0.43704|0.43704	0.1479:0.0:0.0:0.8521|0.1479:0.0:0.0:0.8521	.|.	537|.	Q9H1A4|.	APC1_HUMAN|.	A|C	537|71	.|.	ENSP00000339109:T537A|.	T|Y	-|-	1|2	0|0	ANAPC1|ANAPC1	112324865|112324865	1.000000|1.000000	0.71417|0.71417	0.138000|0.138000	0.22173|0.22173	0.127000|0.127000	0.20565|0.20565	3.555000|3.555000	0.53727|0.53727	0.570000|0.570000	0.29347|0.29347	0.369000|0.369000	0.22263|0.22263	ACT|TAC	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254045.2		-	ENST00000341068.3	Missense_Mutation	SNP	2 : 112608394 - 112608394 C PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	323	4
ARMC7	79637	broad.mit.edu	37	17	73125037	73125037	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr17:73125037C>A	ENST00000581078.1	+	0	774				ARMC7_ENST00000579096.1_3'UTR|ARMC7_ENST00000245543.1_Missense_Mutation_p.F167L			Q9H6L4	ARMC7_HUMAN	armadillo repeat containing 7	NA							binding	p.F167F(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|pancreas(3)	9	all_lung(278;0.14)|Lung NSC(278;0.168)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)			TGGAGGACTTCTGCTCCCCCC	0.701		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				1	Substitution - coding silent(1)	lung(1)											16	16	16			NA	NA	17		NA											NA				73125037		2203	4298	6501	SO:0001624	3_prime_UTR_variant			AK025813	CCDS11714.1	17q25	2013-02-14				ENSG00000125449	79637	79637		Armadillo repeat containing	26168	protein-coding gene	gene with protein product					NA	12477932	Standard	NM_024585	NM_024585	NA	Approved	FLJ22160	uc002jmw.1	Q9H6L4		ENST00000581078.1:c.*125C>A	17.37:g.73125037C>A		NA		37		.	.	.	.	.	.	.	.	.	.	C	12.54	1.969018	0.34754	.	.	ENSG00000125449	ENST00000245543	T	0.32272	1.46	5.18	4.22	0.49857	Armadillo-like helical (1);Armadillo-type fold (1);	0.478366	0.24633	N	0.036863	T	0.18923	0.0454	N	0.16478	0.41	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04017	-1.0984	10	0.35671	T	0.21	.	10.8273	0.46640	0.0:0.7987:0.0:0.2013	.	167	Q9H6L4	ARMC7_HUMAN	L	167	ENSP00000245543:F167L	ENSP00000245543:F167L	F	+	3	2	ARMC7	70636632	1.000000	0.71417	0.968000	0.41197	0.367000	0.29736	2.074000	0.41529	1.338000	0.45544	-0.137000	0.14449	TTC	ARMC7-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000445843.1		+	ENST00000581078.1	3'UTR	SNP	17 : 73125037 - 73125037 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	86	18
ASL	435	broad.mit.edu	37	7	65557066	65557066	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr7:65557066G>A	ENST00000304874.9	+	15	1238	c.1136G>A	c.(1135-1137)cGc>cAc	p.R379H	ASL_ENST00000380839.4_Missense_Mutation_p.R353H|ASL_ENST00000464970.1_3'UTR|ASL_ENST00000395332.3_Missense_Mutation_p.R379H|AC068533.7_ENST00000450043.1_Silent_p.P147P|ASL_ENST00000395331.3_Missense_Mutation_p.R359H	NM_000048.3	NP_000039.2	P04424	ARLY_HUMAN	argininosuccinate lyase	379			R -> C (in ARGINSA; dbSNP:rs28940287).		arginine biosynthetic process via ornithine|arginine catabolic process|urea cycle	cytosol	argininosuccinate lyase activity	p.R379L(1)		breast(3)|endometrium(3)|large_intestine(2)|lung(9)|upper_aerodigestive_tract(1)	18					L-Arginine(DB00125)	TACCTGGTCCGCAAAGGGGTA	0.637		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)											95	92	93			NA	NA	7		NA											NA				65557066		2203	4300	6503	SO:0001583	missense				CCDS5531.1, CCDS47597.1, CCDS47598.1	7q11.21	2012-10-02			ENSG00000126522	ENSG00000126522	435	435	4.3.2.1		746	protein-coding gene	gene with protein product		608310			NA		Standard	NM_000048	NM_001024943	NA	Approved		uc003tuo.3	P04424	OTTHUMG00000022876	ENST00000304874.9:c.1136G>A	7.37:g.65557066G>A	ENSP00000307188:p.Arg379His	NA	Q6LDS5|Q96HS2	37	CCDS5531.1	.	.	.	.	.	.	.	.	.	.	g	27.0	4.786704	0.90367	.	.	ENSG00000126522	ENST00000304874;ENST00000380839;ENST00000395332;ENST00000395331	D;D;D;D	0.91464	-2.85;-2.85;-2.85;-2.85	5.5	4.63	0.57726	L-Aspartase-like (1);	0.000000	0.85682	D	0.000000	D	0.92909	0.7744	M	0.89601	3.045	0.58432	D	0.999999	P;P;B	0.42871	0.792;0.6;0.445	B;B;B	0.43838	0.433;0.077;0.102	D	0.93527	0.6866	10	0.87932	D	0	.	13.5557	0.61757	0.0753:0.0:0.9247:0.0	.	353;359;379	E9PE48;E7EMI0;P04424	.;.;ARLY_HUMAN	H	379;353;379;359	ENSP00000307188:R379H;ENSP00000370219:R353H;ENSP00000378741:R379H;ENSP00000378740:R359H	ENSP00000307188:R379H	R	+	2	0	ASL	65194501	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.997000	0.63921	1.327000	0.45338	0.491000	0.48974	CGC	ASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251695.2		+	ENST00000304874.9	Missense_Mutation	SNP	7 : 65557066 - 65557066 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	472	5
ASTN1	460	broad.mit.edu	37	1	176926840	176926840	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr1:176926840G>A	ENST00000367657.3	-	11	2051	c.1861C>T	c.(1861-1863)Cgc>Tgc	p.R621C	ASTN1_ENST00000424564.2_Missense_Mutation_p.R621C|ASTN1_ENST00000367654.3_Missense_Mutation_p.R629C|ASTN1_ENST00000361833.2_Missense_Mutation_p.R621C|ASTN1_ENST00000281881.3_5'UTR			O14525	ASTN1_HUMAN	astrotactin 1	629	EGF-like 2.				cell migration|neuron cell-cell adhesion	integral to membrane				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						TCCAGCTTGCGATCTGAAATA	0.537		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													85	81	83			NA	NA	1		NA											NA				176926840		2203	4300	6503	SO:0001583	missense			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092	460	460			773	protein-coding gene	gene with protein product		600904	astrotactin	ASTN	NA	9070947	Standard	NM_004319	NM_001286164	NA	Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367657.3:c.1861C>T	1.37:g.176926840G>A	ENSP00000356629:p.Arg621Cys	NA	O60799|Q5W0V7|Q5W0V8	37		.	.	.	.	.	.	.	.	.	.	G	32	5.191818	0.94923	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	D;D;T;D	0.87571	-2.27;-2.27;2.64;-2.27	5.58	5.58	0.84498	Epidermal growth factor-like (1);	0.000000	0.85682	D	0.000000	D	0.90363	0.6984	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.992;0.992	D	0.91468	0.5194	10	0.87932	D	0	-28.5238	19.1684	0.93567	0.0:0.0:1.0:0.0	.	629;621;621	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	C	621;621;629;621;621	ENSP00000356629:R621C;ENSP00000354536:R621C;ENSP00000356626:R629C;ENSP00000395041:R621C	ENSP00000354536:R621C	R	-	1	0	ASTN1	175193463	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.296000	0.96104	2.618000	0.88619	0.563000	0.77884	CGC	ASTN1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000084823.1		-	ENST00000367657.3	Missense_Mutation	SNP	1 : 176926840 - 176926840 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	292	85
ATP13A2	23400	broad.mit.edu	37	1	17322564	17322564	+	Silent	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr1:17322564G>A	ENST00000452699.1	-	15	1623	c.1434C>T	c.(1432-1434)taC>taT	p.Y478Y	ATP13A2_ENST00000341676.5_Silent_p.Y478Y|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000326735.8_Silent_p.Y483Y|ATP13A2_ENST00000502860.1_5'UTR	NM_001141973.1|NM_022089.2	NP_001135445.1|NP_071372.1	Q9NQ11	AT132_HUMAN	ATPase type 13A2	483					ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		GGCTCTGGGCGTAGAGCGTGC	0.622		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													97	102	100			NA	NA	1		NA											NA				17322564		2203	4300	6503	SO:0001819	synonymous_variant			AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363	23400	23400		ATPases / P-type, Parkinson disease	30213	protein-coding gene	gene with protein product		610513	Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)	PARK9	NA	15381061, 16964263	Standard	NM_022089	XM_005245809	NA	Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000452699.1:c.1434C>T	1.37:g.17322564G>A		NA	O75700|Q5JXY2	37	CCDS44073.1																																																																																			ATP13A2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368161.1		-	ENST00000452699.1	Silent	SNP	1 : 17322564 - 17322564 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	511	5
ATXN2L	11273	broad.mit.edu	37	16	28844418	28844418	+	Silent	SNP	T	T	C			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	T	T	-	-	T	T	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr16:28844418T>C	ENST00000564304.1	+	14	1881	c.1716T>C	c.(1714-1716)ccT>ccC	p.P572P	ATXN2L_ENST00000395547.2_Silent_p.P566P|ATXN2L_ENST00000325215.6_Silent_p.P566P|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000336783.4_Silent_p.P566P|ATXN2L_ENST00000570200.1_Silent_p.P566P|ATXN2L_ENST00000340394.8_Silent_p.P566P|ATXN2L_ENST00000382686.4_Silent_p.P566P			Q8WWM7	ATX2L_HUMAN	ataxin 2-like	566						membrane				breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						GCCTGGATCCTTTTCCTCCCC	0.532		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													121	126	125			NA	NA	16		NA											NA				28844418		2197	4300	6497	SO:0001819	synonymous_variant				CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488	11273	11273			31326	protein-coding gene	gene with protein product		607931			NA	11784712, 14769358	Standard	NM_007245	NM_007245	NA	Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000564304.1:c.1716T>C	16.37:g.28844418T>C		NA	B9EGM2|O95135|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	37																																																																																				ATXN2L-008	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000432048.1		+	ENST00000564304.1	Silent	SNP	16 : 28844418 - 28844418 C PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	584	5
CACNG2	10369	broad.mit.edu	37	22	36960760	36960760	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr22:36960760G>A	ENST00000300105.6	-	4	1591	c.610C>T	c.(610-612)Cgg>Tgg	p.R204W		NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	204					membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						TGTTTGTGCCGGTCGATAAAC	0.627		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													99	115	110			NA	NA	22		NA											NA				36960760		2203	4300	6503	SO:0001583	missense			AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862	10369	10369		Calcium channel subunits	1406	protein-coding gene	gene with protein product		602911			NA		Standard		NM_006078	NA	Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.610C>T	22.37:g.36960760G>A	ENSP00000300105:p.Arg204Trp	NA	Q2M1M1|Q5TGT3|Q9UGZ7	37	CCDS13931.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.964618	0.74131	.	.	ENSG00000166862	ENST00000300105	T	0.41065	1.01	5.47	5.47	0.80525	.	0.124937	0.56097	D	0.000032	T	0.60830	0.2299	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	P	0.62014	0.897	T	0.63093	-0.6714	10	0.87932	D	0	-9.67	19.3133	0.94199	0.0:0.0:1.0:0.0	.	204	Q9Y698	CCG2_HUMAN	W	204	ENSP00000300105:R204W	ENSP00000300105:R204W	R	-	1	2	CACNG2	35290706	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.488000	0.81441	2.575000	0.86900	0.655000	0.94253	CGG	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075500.2		-	ENST00000300105.6	Missense_Mutation	SNP	22 : 36960760 - 36960760 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	960	7
CDH24	64403	broad.mit.edu	37	14	23517662	23517662	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr14:23517662G>A	ENST00000267383.5	-	12	2079	c.1987C>T	c.(1987-1989)Cgg>Tgg	p.R663W	CDH24_ENST00000554034.1_Missense_Mutation_p.R625W|CDH24_ENST00000397359.3_Missense_Mutation_p.R663W|CDH24_ENST00000485922.1_5'UTR|CDH24_ENST00000487137.2_Missense_Mutation_p.R625W			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	663					adherens junction organization|cell junction assembly|cell-cell adhesion|homophilic cell adhesion	cell-cell junction|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|delta-catenin binding			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		TTCTGCCGCCGCAGGGCCACG	0.672		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													52	56	55			NA	NA	14		NA											NA				23517662		2202	4295	6497	SO:0001583	missense			AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880	64403	64403		Cadherins / Major cadherins	14265	protein-coding gene	gene with protein product			cadherin-like 24		NA	12734196	Standard	NM_022478	NM_022478	NA	Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.1987C>T	14.37:g.23517662G>A	ENSP00000267383:p.Arg663Trp	NA	D3DS44|Q86UP1|Q9NT84	37	CCDS9585.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.036370	0.54896	.	.	ENSG00000139880	ENST00000397359;ENST00000487137;ENST00000422751;ENST00000554034;ENST00000267383	D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16	4.06	3.13	0.36017	Cadherin, cytoplasmic domain (1);	0.000000	0.64402	D	0.000001	D	0.93759	0.8005	M	0.90309	3.105	0.51767	D	0.999935	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93914	0.7199	10	0.87932	D	0	.	11.5441	0.50683	0.0:0.0:0.8126:0.1874	.	625;663	Q86UP0-2;Q86UP0	.;CAD24_HUMAN	W	663;625;158;625;663	ENSP00000380517:R663W;ENSP00000434821:R625W;ENSP00000452493:R625W;ENSP00000267383:R663W	ENSP00000267383:R663W	R	-	1	2	CDH24	22587502	0.999000	0.42202	1.000000	0.80357	0.657000	0.38888	0.679000	0.25291	0.863000	0.35553	0.591000	0.81541	CGG	CDH24-006	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257241.2		-	ENST00000267383.5	Missense_Mutation	SNP	14 : 23517662 - 23517662 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	415	6
CDH26	60437	broad.mit.edu	37	20	58574705	58574705	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr20:58574705C>T	ENST00000348616.4	+	14	2384	c.2084C>T	c.(2083-2085)aCg>aTg	p.T695M	CDH26_ENST00000244047.5_Missense_Mutation_p.T695M|CDH26_ENST00000350849.6_Missense_Mutation_p.T28M|CDH26_ENST00000497614.1_3'UTR|CDH26_ENST00000244049.3_Missense_Mutation_p.T28M	NM_177980.2	NP_817089.1	Q8IXH8	CAD26_HUMAN	cadherin 26	695					homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			GCAGGACCCACGCAGGGAGTT	0.522		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0								C	MET/THR,MET/THR	2,4404	4.2+/-10.8	0,2,2201	84	81	82		83,2084	-5.8	0	20		82	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CDH26	NM_021810.4,NM_177980.2	81,81	0,3,6500	TT,TC,CC	NA	0.0116,0.0454,0.0231	possibly-damaging,possibly-damaging	28/166,695/833	58574705	3,13003	2203	4300	6503	SO:0001583	missense			AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215	60437	60437		Cadherins / Major cadherins	15902	protein-coding gene	gene with protein product			cadherin-like 26		NA		Standard	NM_177980	NM_177980	NA	Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000348616.4:c.2084C>T	20.37:g.58574705C>T	ENSP00000339390:p.Thr695Met	NA	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	37	CCDS13485.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.687|2.687	-0.274118|-0.274118	0.05679|0.05679	4.54E-4|4.54E-4	1.16E-4|1.16E-4	ENSG00000124215|ENSG00000124215	ENST00000370991|ENST00000244047;ENST00000348616;ENST00000244049;ENST00000350849;ENST00000456106	.|T;T;T	.|0.59638	.|0.25;0.54;0.54	2.88|2.88	-5.76|-5.76	0.02376|0.02376	.|.	.|.	.|.	.|.	.|.	T|T	0.22704|0.22704	0.0548|0.0548	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|P;P;P;B	.|0.43024	.|0.798;0.798;0.474;0.434	.|B;B;B;B	.|0.32465	.|0.094;0.146;0.032;0.07	T|T	0.20940|0.20940	-1.0260|-1.0260	5|9	.|0.34782	.|T	.|0.22	.|.	2.0821|2.0821	0.03637|0.03637	0.2073:0.422:0.0986:0.2721|0.2073:0.422:0.0986:0.2721	.|.	.|28;28;695;695	.|Q8IXH8-5;Q8IXH8-2;Q8IXH8;Q8IXH8-4	.|.;.;CAD26_HUMAN;.	C|M	287|695;695;28;28;28	.|ENSP00000244047:T695M;ENSP00000339390:T695M;ENSP00000310845:T28M	.|ENSP00000244047:T695M	R|T	+|+	1|2	0|0	CDH26|CDH26	58008100|58008100	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-2.002000|-2.002000	0.01464|0.01464	-1.744000|-1.744000	0.01338|0.01338	-3.845000|-3.845000	0.00018|0.00018	CGC|ACG	CDH26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079933.2		+	ENST00000348616.4	Missense_Mutation	SNP	20 : 58574705 - 58574705 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	332	58
CDKN2A	1029	broad.mit.edu	37	9	21971186	21971186	+	Nonsense_Mutation	SNP	G	G	A	rs121913387		TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr9:21971186G>A	ENST00000479692.2	-	2	33	c.19C>T	c.(19-21)Cga>Tga	p.R7*	RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000530628.2_Missense_Mutation_p.P72L|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R58*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P113L|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R58*|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000304494.5_Nonsense_Mutation_p.R58*|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R7*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P72L|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R58*			P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	58					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.R58*(78)|p.?(45)|p.M53_R58del(3)|p.P113L(3)|p.R58fs*59(2)|p.M54fs*61(2)|p.R58fs*88(2)|p.0(1)|p.V28_V51del(1)|p.A57_R58>V*(1)|p.P113fs*>61(1)|p.R58fs*62(1)|p.R58fs*61(1)|p.G55fs*86(1)|p.R58R(1)|p.A57fs*85(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)		TCCGCCACTCGGGCGCTGCCC	0.677		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				1459	Whole gene deletion(1316)|Substitution - Nonsense(78)|Unknown(45)|Deletion - Frameshift(10)|Deletion - In frame(4)|Substitution - Missense(3)|Insertion - Frameshift(1)|Substitution - coding silent(1)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(284)|skin(201)|central_nervous_system(167)|lung(154)|urinary_tract(94)|upper_aerodigestive_tract(78)|bone(74)|oesophagus(65)|soft_tissue(58)|pleura(51)|ovary(38)|pancreas(37)|kidney(32)|breast(32)|stomach(14)|thyroid(13)|NS(12)|biliary_tract(12)|autonomic_ganglia(7)|liver(7)|meninges(7)|large_intestine(6)|salivary_gland(4)|thymus(4)|endometrium(3)|vulva(2)|prostate(2)|cervix(1)	GRCh37	CM940227	CDKN2A	M	rs121913387						7	9	8			NA	NA	9		NA											NA				21971186		2034	4092	6126	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.19C>T	9.37:g.21971186G>A	ENSP00000466887:p.Arg7*	NA	D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.1|28.1	4.893482|4.893482	0.91889|0.91889	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177	T;T|.	0.75367|.	-0.93;-0.89|.	5.79|5.79	2.71|2.71	0.32032|0.32032	.|.	0.409080|.	0.18162|.	N|.	0.149742|.	T|.	0.29288|.	0.0729|.	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	P|.	0.44006|.	0.824|.	B|.	0.33121|.	0.158|.	T|.	0.21381|.	-1.0247|.	10|.	0.72032|0.13470	D|T	0.01|0.59	-3.0019|-3.0019	9.6681|9.6681	0.39996|0.39996	0.0:0.1288:0.474:0.3972|0.0:0.1288:0.474:0.3972	.|.	113|.	Q8N726|.	CD2A2_HUMAN|.	L|X	113;72|58	ENSP00000355153:P113L;ENSP00000432664:P72L|.	ENSP00000355153:P113L|ENSP00000307101:R58X	P|R	-|-	2|1	0|2	CDKN2A|CDKN2A	21961186|21961186	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.277000|0.277000	0.26821|0.26821	0.096000|0.096000	0.15147|0.15147	0.738000|0.738000	0.32606|0.32606	0.555000|0.555000	0.69702|0.69702	CCG|CGA	CDKN2A-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000051922.3		-	ENST00000479692.2	Nonsense_Mutation	SNP	9 : 21971186 - 21971186 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	89	20
CNTN3	5067	broad.mit.edu	37	3	74351867	74351867	+	Nonsense_Mutation	SNP	G	G	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr3:74351867G>T	ENST00000263665.6	-	13	1787	c.1760C>A	c.(1759-1761)tCa>tAa	p.S587*		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	587	Ig-like C2-type 6.				cell adhesion	anchored to membrane|plasma membrane	protein binding			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		AGCAGCAGATGAAACACTGTC	0.418		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													118	100	106			NA	NA	3		NA											NA				74351867		2203	4300	6503	SO:0001587	stop_gained			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805	5067	5067		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	2173	protein-coding gene	gene with protein product		601325		PANG	NA	8661054, 8586965	Standard	NM_020872	XM_005264757	NA	Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.1760C>A	3.37:g.74351867G>T	ENSP00000263665:p.Ser587*	NA	B9EK50|Q9H039	37	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	G	38	6.834241	0.97873	.	.	ENSG00000113805	ENST00000263665	.	.	.	5.08	5.08	0.68730	.	0.136971	0.51477	D	0.000086	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.9949	0.86365	0.0:0.0:1.0:0.0	.	.	.	.	X	587	.	ENSP00000263665:S587X	S	-	2	0	CNTN3	74434557	1.000000	0.71417	0.403000	0.26384	0.815000	0.46073	6.862000	0.75484	2.523000	0.85059	0.585000	0.79938	TCA	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352306.1		-	ENST00000263665.6	Nonsense_Mutation	SNP	3 : 74351867 - 74351867 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	117	28
CNTN3	5067	broad.mit.edu	37	3	74351868	74351868	+	Missense_Mutation	SNP	A	A	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	A	A	-	-	A	A	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr3:74351868A>T	ENST00000263665.6	-	13	1786	c.1759T>A	c.(1759-1761)Tca>Aca	p.S587T		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	587	Ig-like C2-type 6.				cell adhesion	anchored to membrane|plasma membrane	protein binding			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		GCAGCAGATGAAACACTGTCC	0.418		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													119	101	107			NA	NA	3		NA											NA				74351868		2203	4300	6503	SO:0001583	missense			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805	5067	5067		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	2173	protein-coding gene	gene with protein product		601325		PANG	NA	8661054, 8586965	Standard	NM_020872	XM_005264757	NA	Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.1759T>A	3.37:g.74351868A>T	ENSP00000263665:p.Ser587Thr	NA	B9EK50|Q9H039	37	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	A	17.58	3.425150	0.62733	.	.	ENSG00000113805	ENST00000263665	T	0.64991	-0.13	5.08	5.08	0.68730	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.136971	0.51477	D	0.000086	T	0.60702	0.2289	L	0.53249	1.67	0.46749	D	0.999185	P	0.35192	0.489	B	0.41691	0.364	T	0.60806	-0.7190	10	0.38643	T	0.18	.	10.7556	0.46234	0.8287:0.1713:0.0:0.0	.	587	Q9P232	CNTN3_HUMAN	T	587	ENSP00000263665:S587T	ENSP00000263665:S587T	S	-	1	0	CNTN3	74434558	1.000000	0.71417	0.433000	0.26760	0.861000	0.49209	4.988000	0.63863	2.039000	0.60335	0.477000	0.44152	TCA	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352306.1		-	ENST00000263665.6	Missense_Mutation	SNP	3 : 74351868 - 74351868 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	118	28
CORO2A	7464	broad.mit.edu	37	9	100895363	100895363	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr9:100895363C>T	ENST00000343933.5	-	5	862	c.605G>A	c.(604-606)cGc>cAc	p.R202H	CORO2A_ENST00000375077.4_Missense_Mutation_p.R202H	NM_003389.3	NP_003380.3	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	202					actin cytoskeleton organization|intracellular signal transduction	actin cytoskeleton|transcriptional repressor complex	actin filament binding			endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|skin(4)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				CCGAATCTTGCGGTCTTTGCA	0.582		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													195	163	174			NA	NA	9		NA											NA				100895363		2203	4300	6503	SO:0001583	missense			U57057	CCDS6735.1	9q22.3	2013-01-10	2001-11-28		ENSG00000106789	ENSG00000106789	7464	7464		Coronins, WD repeat domain containing	2255	protein-coding gene	gene with protein product	coronin 2A, coronin-like protein B, WD protein IR10, WD-repeat protein 2	602159	coronin, actin-binding protein, 2A		NA	8985118	Standard	NM_003389	NM_052820	NA	Approved	IR10, WDR2	uc004aym.3	Q92828	OTTHUMG00000020340	ENST00000343933.5:c.605G>A	9.37:g.100895363C>T	ENSP00000343746:p.Arg202His	NA	Q5TBR5|Q92829|Q9BWS5	37	CCDS6735.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.660467	0.88154	.	.	ENSG00000106789	ENST00000343933;ENST00000375077	T;T	0.61040	0.14;0.14	4.94	4.05	0.47172	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.095153	0.64402	D	0.000002	T	0.67822	0.2934	L	0.47190	1.495	0.45490	D	0.998457	D	0.89917	1.0	D	0.74023	0.982	T	0.70626	-0.4820	10	0.87932	D	0	-18.4897	12.2613	0.54652	0.0:0.9162:0.0:0.0838	.	202	Q92828	COR2A_HUMAN	H	202	ENSP00000343746:R202H;ENSP00000364218:R202H	ENSP00000343746:R202H	R	-	2	0	CORO2A	99935184	0.070000	0.21116	1.000000	0.80357	0.994000	0.84299	0.551000	0.23361	1.314000	0.45095	0.655000	0.94253	CGC	CORO2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053357.1		-	ENST00000343933.5	Missense_Mutation	SNP	9 : 100895363 - 100895363 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	411	5
CXCR2	3579	broad.mit.edu	37	2	219000390	219000390	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr2:219000390G>A	ENST00000318507.2	+	3	1293	c.866G>A	c.(865-867)cGc>cAc	p.R289H		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	289					activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cellular defense response|dendritic cell chemotaxis|inflammatory response|neutrophil activation|neutrophil chemotaxis|positive regulation of cell proliferation	cell surface|integral to plasma membrane|mast cell granule	interleukin-8 receptor activity			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						TGTGAGCGCCGCAATCACATC	0.597		NA											G	1	5e-04	NA	NA	2184	0.0017	0.9999	,	,	NA	3e-04	NA	NA	NA	5e-04	0.9181	LOWCOV,EXOME	NA	NA	5e-04	SNP								NA				0													83	78	79			NA	NA	2		NA											NA				219000390		2203	4300	6503	SO:0001583	missense			U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871	3579	3579		CD molecules, GPCR / Class A : Chemokine receptors : C-X-C motif, Interleukins and interleukin receptors	6027	protein-coding gene	gene with protein product		146928	interleukin 8 receptor, beta	IL8RB	NA	1427896	Standard	NM_001557	NM_001557	NA	Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.866G>A	2.37:g.219000390G>A	ENSP00000319635:p.Arg289His	NA	Q8IUZ1|Q9P2T6|Q9P2T7	37	CCDS2408.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	13.03	2.114961	0.37339	.	.	ENSG00000180871	ENST00000318507	T	0.37411	1.2	5.36	4.47	0.54385	GPCR, rhodopsin-like superfamily (1);	0.057955	0.64402	D	0.000006	T	0.48502	0.1503	M	0.70108	2.13	0.09310	N	0.999998	P	0.38767	0.646	P	0.50231	0.635	T	0.40440	-0.9563	9	.	.	.	.	9.7981	0.40748	0.1635:0.0:0.8365:0.0	.	289	P25025	CXCR2_HUMAN	H	289	ENSP00000319635:R289H	.	R	+	2	0	CXCR2	218708635	0.930000	0.31532	0.358000	0.25811	0.045000	0.14185	3.615000	0.54167	1.243000	0.43853	0.456000	0.33151	CGC	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256772.2		+	ENST00000318507.2	Missense_Mutation	SNP	2 : 219000390 - 219000390 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	300	5
DHRS2	10202	broad.mit.edu	37	14	24114078	24114078	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr14:24114078C>A	ENST00000250383.6	+	8	1194	c.718C>A	c.(718-720)Cat>Aat	p.H240N	DHRS2_ENST00000344777.7_Silent_p.I243I	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2	218					C21-steroid hormone metabolic process|cellular response to oxidative stress|myeloid dendritic cell differentiation|negative regulation of apoptosis|negative regulation of cell proliferation|response to toxin	mitochondrion|nuclear envelope	binding|carbonyl reductase (NADPH) activity			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		CAAGGAACATCATCAGCTGCA	0.512		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													106	106	106			NA	NA	14		NA											NA				24114078		2203	4300	6503	SO:0001583	missense				CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867	10202	10202		Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1	18349	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase family 25C, member 1	615194			NA	7556196, 11944995, 16685466, 19027726	Standard	NM_182908	NM_182908	NA	Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.718C>A	14.37:g.24114078C>A	ENSP00000250383:p.His240Asn	NA	Q53GS4|Q7Z789|Q9H2R2	37	CCDS9604.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.123|8.123	0.781271|0.781271	0.16120|0.16120	.|.	.|.	ENSG00000100867|ENSG00000100867	ENST00000250383;ENST00000553600|ENST00000557535	D;T|.	0.87966|.	-2.32;1.02|.	5.48|5.48	-5.45|-5.45	0.02616|0.02616	.|.	.|.	.|.	.|.	.|.	T|.	0.18676|.	0.0448|.	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999999|0.999999	B|.	0.32010|.	0.351|.	B|.	0.27380|.	0.079|.	T|.	0.27400|.	-1.0075|.	8|.	0.54805|.	T|.	0.06|.	.|.	3.8079|3.8079	0.08785|0.08785	0.1079:0.2756:0.1063:0.5103|0.1079:0.2756:0.1063:0.5103	.|.	240|.	D3DS54|.	.|.	N|X	240;140|139	ENSP00000250383:H240N;ENSP00000451485:H140N|.	ENSP00000250383:H240N|.	H|S	+|+	1|2	0|0	DHRS2|DHRS2	23183918|23183918	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-1.335000|-1.335000	0.02662|0.02662	-1.100000|-1.100000	0.03030|0.03030	-1.098000|-1.098000	0.02139|0.02139	CAT|TCA	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000071842.2		+	ENST00000250383.6	Missense_Mutation	SNP	14 : 24114078 - 24114078 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	268	46
DNAH11	8701	broad.mit.edu	37	7	21657266	21657266	+	Silent	SNP	C	C	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr7:21657266C>A	ENST00000409508.3	+	23	4156	c.4125C>A	c.(4123-4125)cgC>cgA	p.R1375R	DNAH11_ENST00000328843.6_Silent_p.R1380R	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1380	Stem (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						AGGAAGTCCGCGTCTGGGATG	0.483		NA							Kartagener syndrome					NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													54	54	54			NA	NA	7		NA											NA				21657266		1882	4106	5988	SO:0001819	synonymous_variant	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04				8701	8701		Axonemal dyneins	2942	protein-coding gene	gene with protein product	dynein, ciliary, heavy chain 11, dynein, heavy chain beta-like	603339	dynein, axonemal, heavy polypeptide 11		NA	9256245	Standard	NM_003777	NM_001277115	NA	Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.4125C>A	7.37:g.21657266C>A		NA	Q9UJ82	37																																																																																				DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000326582.6		+	ENST00000409508.3	Silent	SNP	7 : 21657266 - 21657266 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	133	28
DVL3	1857	broad.mit.edu	37	3	183884692	183884692	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr3:183884692G>A	ENST00000313143.3	+	11	1375	c.1127G>A	c.(1126-1128)gGc>gAc	p.G376D	DVL3_ENST00000431765.1_Missense_Mutation_p.G359D|EIF2B5_ENST00000444495.1_Intron	NM_004423.3	NP_004414.3	Q92997	DVL3_HUMAN	dishevelled segment polarity protein 3	376					canonical Wnt receptor signaling pathway|intracellular signal transduction|positive regulation of JUN kinase activity|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent	cytoplasm	beta-catenin binding|frizzled binding|protease binding|protein heterodimerization activity|signal transducer activity			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(6)|liver(1)|lung(13)|ovary(1)|prostate(1)	35	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)			CCTGCATACGGCATGAGCCCC	0.647		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													127	119	122			NA	NA	3		NA											NA				183884692		2203	4300	6503	SO:0001583	missense			D86963	CCDS3253.1	3q27	2013-05-22	2013-05-22		ENSG00000161202	ENSG00000161202	1857	1857		Dishevelled homologs	3087	protein-coding gene	gene with protein product		601368	dishevelled 3 (homologous to Drosophila dsh), dishevelled, dsh homolog 3 (Drosophila)		NA	8817329	Standard	NM_004423	NM_004423	NA	Approved	KIAA0208	uc003fms.3	Q92997	OTTHUMG00000156841	ENST00000313143.3:c.1127G>A	3.37:g.183884692G>A	ENSP00000316054:p.Gly376Asp	NA	D3DNT0|O14642|Q13531|Q8N5E9|Q92607	37	CCDS3253.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.398229	0.83120	.	.	ENSG00000161202	ENST00000313143;ENST00000415612;ENST00000431765	T;T	0.04156	3.71;3.69	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.16557	0.0398	M	0.68593	2.085	0.80722	D	1	P;P;B;D	0.57257	0.94;0.94;0.232;0.979	P;P;B;P	0.55222	0.694;0.76;0.113;0.771	T	0.00172	-1.1958	10	0.33141	T	0.24	-34.8595	20.4387	0.99107	0.0:0.0:1.0:0.0	.	359;208;376;376	B4E3E5;Q9UG07;F5GWR8;Q92997	.;.;.;DVL3_HUMAN	D	376;376;359	ENSP00000316054:G376D;ENSP00000405885:G359D	ENSP00000316054:G376D	G	+	2	0	DVL3	185367386	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.008000	0.88588	2.836000	0.97738	0.655000	0.94253	GGC	DVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346184.1		+	ENST00000313143.3	Missense_Mutation	SNP	3 : 183884692 - 183884692 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	462	6
F5	2153	broad.mit.edu	37	1	169510405	169510405	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr1:169510405C>A	ENST00000367796.3	-	13	4139	c.3938G>T	c.(3937-3939)aGt>aTt	p.S1313I	F5_ENST00000367797.3_Missense_Mutation_p.S1308I			P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1308	35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.				cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	GTTTGTCTGACTGAGTTCTGG	0.512		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													272	296	288			NA	NA	1		NA											NA				169510405		2203	4300	6503	SO:0001583	missense			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734	2153	2153			3542	protein-coding gene	gene with protein product		612309			NA		Standard	NM_000130	NM_000130	NA	Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367796.3:c.3938G>T	1.37:g.169510405C>A	ENSP00000356770:p.Ser1313Ile	NA	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	37		.	.	.	.	.	.	.	.	.	.	C	12.19	1.864337	0.32977	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.35789	1.29;1.29	3.21	-2.1	0.07210	.	1.723450	0.02512	N	0.091650	T	0.13372	0.0324	L	0.55990	1.75	0.22199	N	0.999294	P	0.45283	0.855	B	0.38327	0.271	T	0.14008	-1.0488	9	0.40728	T	0.16	.	5.0898	0.14702	0.0:0.4556:0.315:0.2294	.	1308	P12259	FA5_HUMAN	I	1308;1313	ENSP00000356771:S1308I;ENSP00000356770:S1313I	ENSP00000356770:S1313I	S	-	2	0	F5	167777029	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.937000	0.00685	-0.282000	0.09128	0.542000	0.68232	AGT	F5-002	NOVEL	not_organism_supported|basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000083713.1		-	ENST00000367796.3	Missense_Mutation	SNP	1 : 169510405 - 169510405 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	1153	7
FAT3	120114	broad.mit.edu	37	11	92531377	92531377	+	Missense_Mutation	SNP	G	G	A	rs150673105	by1000genomes	TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr11:92531377G>A	ENST00000525166.1	+	9	4770	c.4748G>A	c.(4747-4749)cGc>cAc	p.R1583H	FAT3_ENST00000298047.6_Missense_Mutation_p.R1733H|FAT3_ENST00000409404.2_Missense_Mutation_p.R1733H			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1733	Cadherin 15.				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GATTATGAGCGCACATCCTCT	0.408		NA								TCGA Ovarian(4;0.039)			g	11	0.01	0.02	NA	2184	NA	0.9995	,	,	NA	4e-04	NA	NA	NA	0.0053	0.9657	LOWCOV	NA	NA	4e-04	SNP								NA				0								A	HIS/ARG	33,3907		0,33,1937	90	87	88		5198	-3	0	11	dbSNP_134	88	1,8327		0,1,4163	yes	missense	FAT3	NM_001008781.2	29	0,34,6100	AA,AG,GG	NA	0.012,0.8376,0.2771	benign	1733/4558	92531377	34,12234	1970	4164	6134	SO:0001583	missense			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323	120114	120114		Cadherins / Cadherin-related	23112	protein-coding gene	gene with protein product	cadherin-related family member 10	612483	FAT tumor suppressor homolog 3 (Drosophila)		NA	11811999	Standard	NM_001008781	NM_001008781	NA	Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000525166.1:c.4748G>A	11.37:g.92531377G>A	ENSP00000432586:p.Arg1583His	NA	B5MDB0|Q96AU6	37		11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	g	10.46	1.355966	0.24598	0.008376	1.2E-4	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.51574	0.7;0.7;0.7	5.93	-2.98	0.05513	.	.	.	.	.	T	0.17916	0.0430	L	0.33710	1.025	0.46279	D	0.998966	B	0.12013	0.005	B	0.04013	0.001	T	0.02352	-1.1172	9	0.39692	T	0.17	.	10.5459	0.45060	0.6862:0.0:0.2094:0.1044	.	1733	Q8TDW7-3	.	H	1733;1733;1583	ENSP00000298047:R1733H;ENSP00000387040:R1733H;ENSP00000432586:R1583H	ENSP00000298047:R1733H	R	+	2	0	FAT3	92171025	0.003000	0.15002	0.005000	0.12908	0.890000	0.51754	0.054000	0.14205	-0.910000	0.03847	-0.930000	0.02707	CGC	FAT3-001	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000335363.3		+	ENST00000525166.1	Missense_Mutation	SNP	11 : 92531377 - 92531377 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	249	57
GADL1	339896	broad.mit.edu	37	3	30875345	30875345	+	Splice_Site	SNP	A	A	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	A	A	-	-	A	A	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr3:30875345A>T	ENST00000454381.3	-	11	1096	c.1050T>A	c.(1048-1050)tcT>tcA	p.S350S	GADL1_ENST00000282538.5_Splice_Site_p.S350S			Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	350					carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25					Pyridoxal Phosphate(DB00114)	GAAAACTTACAGATTTGTCTT	0.502		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													72	68	70			NA	NA	3		NA											NA				30875345		2203	4300	6503	SO:0001630	splice_region_variant			AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644	339896	339896			27949	protein-coding gene	gene with protein product		615601			NA		Standard	NM_207359	NM_207359	NA	Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000454381.3:c.1050+1T>A	3.37:g.30875345A>T		NA		37																																																																																				GADL1-002	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000341541.2	Silent	-	ENST00000454381.3	Splice_Site	SNP	3 : 30875345 - 30875345 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	186	38
GRID1	2894	broad.mit.edu	37	10	87407024	87407024	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr10:87407024G>A	ENST00000327946.7	-	13	2213	c.2128C>T	c.(2128-2130)Cgg>Tgg	p.R710W	GRID1_ENST00000536331.1_Missense_Mutation_p.R281W|RP11-93H12.4_ENST00000474115.2_RNA	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	710						cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106					L-Glutamic Acid(DB00142)	CTGATGGTCCGCCAGAGTTCA	0.572		NA								Multiple Myeloma(13;0.14)				NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0								G	TRP/ARG	0,4406		0,0,2203	257	236	243		2128	-5.4	0.9	10		243	2,8598	2.2+/-6.3	0,2,4298	no	missense	GRID1	NM_017551.2	101	0,2,6501	AA,AG,GG	NA	0.0233,0.0,0.0154	probably-damaging	710/1010	87407024	2,13004	2203	4300	6503	SO:0001583	missense			AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771	2894	2894		Ligand-gated ion channels / Glutamate receptors, ionotropic, Glutamate receptors	4575	protein-coding gene	gene with protein product		610659			NA		Standard	XM_043613	NM_017551	NA	Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.2128C>T	10.37:g.87407024G>A	ENSP00000330148:p.Arg710Trp	NA	B3KXD5|Q8IXT3	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.182564	0.78677	0.0	2.33E-4	ENSG00000182771	ENST00000327946;ENST00000536331	T;T	0.26957	1.7;1.7	5.7	-5.39	0.02664	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.143577	0.64402	D	0.000010	T	0.40196	0.1107	M	0.85777	2.775	0.80722	D	1	D	0.57899	0.981	P	0.49887	0.625	T	0.61898	-0.6968	10	0.72032	D	0.01	.	19.1965	0.93691	0.0:0.0:0.6216:0.3784	.	710	Q9ULK0	GRID1_HUMAN	W	710;281	ENSP00000330148:R710W;ENSP00000444455:R281W	ENSP00000330148:R710W	R	-	1	2	GRID1	87397004	1.000000	0.71417	0.902000	0.35471	0.939000	0.58152	1.430000	0.34914	-1.166000	0.02783	-0.271000	0.10264	CGG	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049148.3		-	ENST00000327946.7	Missense_Mutation	SNP	10 : 87407024 - 87407024 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	1057	7
HAP1	9001	broad.mit.edu	37	17	39881075	39881075	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr17:39881075C>T	ENST00000393939.2	-	10	1672	c.1663G>A	c.(1663-1665)Gcc>Acc	p.A555T	HAP1_ENST00000310778.5_Missense_Mutation_p.A632T|JUP_ENST00000540235.1_Intron|HAP1_ENST00000341193.5_Missense_Mutation_p.A563T|HAP1_ENST00000347901.4_Missense_Mutation_p.A580T			P54257	HAP1_HUMAN	huntingtin-associated protein 1	632	Glu-rich.				brain development|protein localization|synaptic transmission	actin cytoskeleton	protein binding			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			TGCCAGTTGGCCAGCTGCTGG	0.627		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													122	123	122			NA	NA	17		NA											NA				39881075		2203	4300	6503	SO:0001583	missense			AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805	9001	9001			4812	protein-coding gene	gene with protein product	neuroan 1	600947		HAP2	NA	7477378, 9668110	Standard	NM_003949	NM_177977	NA	Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000393939.2:c.1663G>A	17.37:g.39881075C>T	ENSP00000377513:p.Ala555Thr	NA	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	37	CCDS42339.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.117571	0.37339	.	.	ENSG00000173805	ENST00000458656;ENST00000442364;ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	T;T;T;T;T;T	0.44881	1.32;0.91;3.15;3.41;3.27;3.16	4.14	2.06	0.26882	.	0.560677	0.15052	N	0.283242	T	0.36138	0.0956	L	0.27053	0.805	0.09310	N	0.99999	P;D;D;D	0.56968	0.872;0.965;0.974;0.978	P;P;P;P	0.54270	0.578;0.546;0.747;0.563	T	0.10064	-1.0646	10	0.32370	T	0.25	-11.1038	4.8636	0.13596	0.219:0.6683:0.0:0.1127	.	555;563;580;632	P54257-3;P54257-4;P54257-2;P54257	.;.;.;HAP1_HUMAN	T	87;49;555;632;580;563	ENSP00000404640:A87T;ENSP00000388981:A49T;ENSP00000377513:A555T;ENSP00000309392:A632T;ENSP00000334002:A580T;ENSP00000343170:A563T	ENSP00000309392:A632T	A	-	1	0	HAP1	37134601	0.215000	0.23574	0.948000	0.38648	0.014000	0.08584	-0.225000	0.09151	0.459000	0.27016	-0.350000	0.07774	GCC	HAP1-007	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389618.1		-	ENST00000393939.2	Missense_Mutation	SNP	17 : 39881075 - 39881075 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	633	7
HLX	3142	broad.mit.edu	37	1	221057751	221057751	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr1:221057751C>T	ENST00000366903.6	+	4	2673	c.1172C>T	c.(1171-1173)aCg>aTg	p.T391M	HLX_ENST00000549319.1_Missense_Mutation_p.T177M	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	391	Ser-rich.				cell differentiation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		CCCAGCGACACGGAGCGGACT	0.642		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													59	52	55			NA	NA	1		NA											NA				221057751		2203	4300	6503	SO:0001583	missense			BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630	3142	3142		Homeoboxes / ANTP class : NKL subclass	4978	protein-coding gene	gene with protein product		142995	H2.0 (Drosophila)-like homeo box 1, H2.0-like homeobox 1 (Drosophila), H2.0-like homeobox 1	HLX1	NA	1676597, 7806220	Standard	NM_021958	NM_021958	NA	Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.1172C>T	1.37:g.221057751C>T	ENSP00000355870:p.Thr391Met	NA	B2R8A8|Q15988|Q59HE7|Q9NZ75	37	CCDS1527.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.952214	0.53293	.	.	ENSG00000136630	ENST00000366903;ENST00000427693;ENST00000549319	D;T;T	0.90385	-2.66;0.51;3.29	5.03	4.09	0.47781	.	0.247697	0.27811	N	0.017749	D	0.84174	0.5414	N	0.24115	0.695	0.09310	N	1	P	0.48640	0.913	B	0.43809	0.432	T	0.77587	-0.2532	10	0.66056	D	0.02	-14.4125	9.6566	0.39930	0.1598:0.6859:0.1543:0.0	.	391	Q14774	HLX_HUMAN	M	391;124;177	ENSP00000355870:T391M;ENSP00000408248:T124M;ENSP00000449882:T177M	ENSP00000355870:T391M	T	+	2	0	HLX	219124374	0.977000	0.34250	0.038000	0.18304	0.737000	0.42083	2.102000	0.41796	1.207000	0.43291	0.561000	0.74099	ACG	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090902.3		+	ENST00000366903.6	Missense_Mutation	SNP	1 : 221057751 - 221057751 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	275	67
HSPA5	3309	broad.mit.edu	37	9	128000914	128000914	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr9:128000914C>T	ENST00000324460.6	-	6	1392	c.1189G>A	c.(1189-1191)Ggt>Agt	p.G397S		NM_005347.4	NP_005338.1	P11021	GRP78_HUMAN	heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)	397					anti-apoptosis|cellular response to glucose starvation|ER-associated protein catabolic process|platelet activation|platelet degranulation|regulation of protein folding in endoplasmic reticulum	cell surface|endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|integral to endoplasmic reticulum membrane|melanosome|midbody|nucleus|perinuclear region of cytoplasm	ATP binding|ATPase activity|calcium ion binding|caspase inhibitor activity|chaperone binding|misfolded protein binding|protein binding, bridging|protein domain specific binding|ubiquitin protein ligase binding|unfolded protein binding			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|prostate(2)|skin(1)	23					Antihemophilic Factor(DB00025)	ACAGCAGCACCATACGCTACA	0.478		NA								Prostate(1;0.17)				NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													105	89	94			NA	NA	9		NA											NA				128000914		2203	4300	6503	SO:0001583	missense				CCDS6863.1	9q33.3	2011-09-02	2002-08-29		ENSG00000044574	ENSG00000044574	3309	3309		Heat shock proteins / HSP70	5238	protein-coding gene	gene with protein product		138120	heat shock 70kD protein 5 (glucose-regulated protein, 78kD)	GRP78	NA		Standard		NM_005347	NA	Approved	BiP	uc004bpn.3	P11021	OTTHUMG00000020672	ENST00000324460.6:c.1189G>A	9.37:g.128000914C>T	ENSP00000324173:p.Gly397Ser	NA	B0QZ61|Q2EF78|Q9NPF1|Q9UK02	37	CCDS6863.1	.	.	.	.	.	.	.	.	.	.	C	33	5.269740	0.95429	.	.	ENSG00000044574	ENST00000324460	T	0.74526	-0.85	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	D	0.93167	0.7824	H	0.99937	4.99	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96722	0.9533	10	0.87932	D	0	-2.7014	16.4549	0.84009	0.0:1.0:0.0:0.0	.	397	P11021	GRP78_HUMAN	S	397	ENSP00000324173:G397S	ENSP00000324173:G397S	G	-	1	0	HSPA5	127040735	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.818000	0.86416	2.097000	0.63578	0.563000	0.77884	GGT	HSPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054062.1		-	ENST00000324460.6	Missense_Mutation	SNP	9 : 128000914 - 128000914 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	274	64
JPH1	56704	broad.mit.edu	37	8	75227310	75227310	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr8:75227310C>T	ENST00000342232.4	-	2	965	c.925G>A	c.(925-927)Gca>Aca	p.A309T		NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	309					calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			TTGTTATTTGCCCACTCCCCT	0.502		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													132	129	130			NA	NA	8		NA											NA				75227310		2203	4300	6503	SO:0001583	missense			AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369	56704	56704			14201	protein-coding gene	gene with protein product		605266			NA	10891348, 10949023	Standard		XM_005251273	NA	Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.925G>A	8.37:g.75227310C>T	ENSP00000344488:p.Ala309Thr	NA	B2RTZ0	37	CCDS6217.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.476800	0.63849	.	.	ENSG00000104369	ENST00000342232	T	0.54279	0.58	5.31	4.4	0.53042	.	0.197272	0.45126	D	0.000382	T	0.40498	0.1119	L	0.39633	1.23	0.43662	D	0.996086	P	0.36354	0.549	B	0.33196	0.159	T	0.20107	-1.0285	10	0.24483	T	0.36	.	12.7522	0.57314	0.0:0.6542:0.3458:0.0	.	309	Q9HDC5	JPH1_HUMAN	T	309	ENSP00000344488:A309T	ENSP00000344488:A309T	A	-	1	0	JPH1	75389865	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	3.773000	0.55333	2.749000	0.94314	0.655000	0.94253	GCA	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379102.1		-	ENST00000342232.4	Missense_Mutation	SNP	8 : 75227310 - 75227310 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	456	5
KDM6B	23135	broad.mit.edu	37	17	7752044	7752044	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr17:7752044G>A	ENST00000254846.5	+	11	2827	c.2438G>A	c.(2437-2439)gGa>gAa	p.G813E	KDM6B_ENST00000448097.2_Missense_Mutation_p.G813E	NM_001080424.1	NP_001073893.1	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	813	Pro-rich.				inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						GTGCTGGAGGGACAAAAGTAC	0.647		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													52	57	56			NA	NA	17		NA											NA				7752044		2202	4300	6502	SO:0001583	missense			AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510	23135	23135		Chromatin-modifying enzymes / K-demethylases	29012	protein-coding gene	gene with protein product		611577	jumonji domain containing 3, jumonji domain containing 3, histone lysine demethylase	JMJD3	NA	10662545, 9205841	Standard	XM_043272	NM_001080424	NA	Approved	KIAA0346	uc002giw.1	O15054		ENST00000254846.5:c.2438G>A	17.37:g.7752044G>A	ENSP00000254846:p.Gly813Glu	NA	C9IZ40|Q96G33	37	CCDS32552.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.958268	0.34565	.	.	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.16897	2.31;2.31	4.54	4.54	0.55810	.	0.242138	0.31092	N	0.008272	T	0.22244	0.0536	N	0.19112	0.55	0.38701	D	0.952991	P;D	0.58268	0.816;0.982	B;P	0.55087	0.311;0.768	T	0.08229	-1.0732	10	0.87932	D	0	-5.6434	16.5716	0.84613	0.0:0.0:1.0:0.0	.	813;813	O15054;O15054-1	KDM6B_HUMAN;.	E	813	ENSP00000254846:G813E;ENSP00000412513:G813E	ENSP00000254846:G813E	G	+	2	0	KDM6B	7692769	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.418000	0.59828	2.526000	0.85167	0.462000	0.41574	GGA	KDM6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440247.1		+	ENST00000254846.5	Missense_Mutation	SNP	17 : 7752044 - 7752044 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	390	113
KIF18A	81930	broad.mit.edu	37	11	28080600	28080600	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr11:28080600C>G	ENST00000263181.6	-	13	2111	c.1821G>C	c.(1819-1821)ttG>ttC	p.L607F		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	607					blood coagulation|microtubule depolymerization|microtubule-based movement|mitotic metaphase plate congression|mitotic prometaphase|protein transport	caveola|cytosol|kinetochore microtubule|microtubule organizing center|nucleus|ruffle	actin binding|ATP binding|microtubule plus-end binding|plus-end-directed microtubule motor activity|tubulin-dependent ATPase activity|ubiquitin binding			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						TCCTCTCTACCAAATGTTCGA	0.408		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													177	175	176			NA	NA	11		NA											NA				28080600		2202	4299	6501	SO:0001583	missense			AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621	81930	81930		Kinesins	29441	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 99	611271			NA	11230166	Standard	NM_031217	NM_031217	NA	Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.1821G>C	11.37:g.28080600C>G	ENSP00000263181:p.Leu607Phe	NA	Q4VPE3|Q86VS5|Q9H0F3	37	CCDS7867.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.524458	0.44969	.	.	ENSG00000121621	ENST00000263181	T	0.77098	-1.07	5.62	0.802	0.18686	.	0.070738	0.56097	D	0.000026	D	0.84215	0.5423	M	0.70275	2.135	0.46521	D	0.999083	D	0.89917	1.0	D	0.73380	0.98	T	0.81701	-0.0813	10	0.51188	T	0.08	.	10.6652	0.45726	0.0:0.2739:0.0:0.7261	.	607	Q8NI77	KI18A_HUMAN	F	607	ENSP00000263181:L607F	ENSP00000263181:L607F	L	-	3	2	KIF18A	28037176	0.986000	0.35501	0.989000	0.46669	0.381000	0.30169	0.007000	0.13174	-0.080000	0.12685	-0.229000	0.12294	TTG	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388328.3		-	ENST00000263181.6	Missense_Mutation	SNP	11 : 28080600 - 28080600 G PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	521	9
KIR3DL1	3811	broad.mit.edu	37	19	55333120	55333120	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr19:55333120G>A	ENST00000391728.4	+	5	789	c.756G>A	c.(754-756)atG>atA	p.M252I	KIR3DL1_ENST00000402254.2_Missense_Mutation_p.M252I|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.M252I|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.M252I|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.M157I|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.M252I	NM_013289.2	NP_037421.2			killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	NA										breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CCTATGACATGTACCATCTAT	0.587		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													16	17	16			NA	NA	19		NA											NA				55333120		2087	4000	6087	SO:0001583	missense			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633	3811	3811		Killer cell immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	6338	protein-coding gene	gene with protein product		604946		KIR	NA	7716543, 7749980	Standard	NM_013289	NM_013289	NA	Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.756G>A	19.37:g.55333120G>A	ENSP00000375608:p.Met252Ile	NA		37	CCDS42621.1	.	.	.	.	.	.	.	.	.	.	-	0.425	-0.906123	0.02453	.	.	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	T;T;T;T;T;T	0.19532	2.14;2.14;2.14;2.14;2.14;2.14	1.47	-2.94	0.05581	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	3.298930	0.01900	N	0.039137	T	0.12390	0.0301	N	0.17594	0.5	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.13407	0.009;0.004;0.001;0.009	T	0.25572	-1.0128	10	0.19147	T	0.46	.	5.1298	0.14903	0.0:0.1775:0.4406:0.3819	.	252;157;252;252	Q15702;Q14946;F6QF33;P43629	.;.;.;KI3L1_HUMAN	I	252;252;252;230;252;252;157	ENSP00000384528:M252I;ENSP00000443350:M252I;ENSP00000442355:M252I;ENSP00000375608:M252I;ENSP00000326868:M252I;ENSP00000350901:M157I	ENSP00000326868:M252I	M	+	3	0	KIR3DL1	60024932	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.385000	0.20685	-3.201000	0.00217	-3.594000	0.00028	ATG	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000141238.1		+	ENST00000391728.4	Missense_Mutation	SNP	19 : 55333120 - 55333120 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	100	55
KLC4	89953	broad.mit.edu	37	6	43039979	43039979	+	Silent	SNP	C	C	A	rs145201350	by1000genomes	TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr6:43039979C>A	ENST00000453940.2	+	11	1323	c.1243C>A	c.(1243-1245)Cgg>Agg	p.R415R	KLC4_ENST00000347162.5_Silent_p.R492R|KLC4_ENST00000479388.1_Silent_p.R492R|KLC4_ENST00000394058.1_Silent_p.R492R|KLC4_ENST00000394056.2_Silent_p.R492R|KLC4_ENST00000259708.3_Silent_p.R510R			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	492						cytoplasm|kinesin complex|microtubule	microtubule motor activity|protein binding			endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			ATGTGCCCTGCGGTCCCGGAG	0.602		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													52	57	55			NA	NA	6		NA											NA				43039979		2203	4300	6503	SO:0001819	synonymous_variant			AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171	89953	89953		Tetratricopeptide (TTC) repeat domain containing	21624	protein-coding gene	gene with protein product			kinesin-like 8	KNSL8	NA		Standard	NM_138343	NM_001289034	NA	Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000453940.2:c.1243C>A	6.37:g.43039979C>A		NA	B3KNY4|B3KPI3|B3KSQ3|Q66K28	37																																																																																				KLC4-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000358142.1		+	ENST00000453940.2	Silent	SNP	6 : 43039979 - 43039979 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	190	4
KLK13	26085	broad.mit.edu	37	19	51561826	51561826	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr19:51561826C>T	ENST00000595793.1	-	4	656	c.614G>A	c.(613-615)gGc>gAc	p.G205D	KLK13_ENST00000335422.3_Missense_Mutation_p.G53D|KLK13_ENST00000595547.1_Missense_Mutation_p.G132D	NM_015596.1	NP_056411.1	Q9UKR3	KLK13_HUMAN	kallikrein-related peptidase 13	205	Peptidase S1.				proteolysis		protein binding|serine-type endopeptidase activity			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	16		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00432)		CTCTTTTGTGCCGGCACACAA	0.527		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													206	186	193			NA	NA	19		NA											NA				51561826		2203	4300	6503	SO:0001583	missense				CCDS12822.1	19q13.33	2008-02-05	2006-10-27			ENSG00000167759	26085	26085		Kallikreins	6361	protein-coding gene	gene with protein product		605505	kallikrein 13		NA	16800724, 16800723	Standard	NM_015596	NM_015596	NA	Approved	KLK-L4	uc002pvn.3	Q9UKR3		ENST00000595793.1:c.614G>A	19.37:g.51561826C>T	ENSP00000470555:p.Gly205Asp	NA	A7UNK6|Q9Y433	37	CCDS12822.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.130091	0.56721	.	.	ENSG00000167759	ENST00000156476;ENST00000335422	D	0.90133	-2.62	4.67	4.67	0.58626	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.136174	0.33732	N	0.004605	D	0.95971	0.8688	M	0.90595	3.13	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.983;0.999;0.999	D	0.96571	0.9423	10	0.87932	D	0	.	15.4416	0.75187	0.0:1.0:0.0:0.0	.	53;132;205	Q86VI8;Q86VI7;Q9UKR3	.;.;KLK13_HUMAN	D	205;53	ENSP00000334079:G53D	ENSP00000156476:G205D	G	-	2	0	KLK13	56253638	0.998000	0.40836	0.858000	0.33744	0.171000	0.22731	6.159000	0.71856	2.588000	0.87417	0.561000	0.74099	GGC	KLK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464298.2		-	ENST00000595793.1	Missense_Mutation	SNP	19 : 51561826 - 51561826 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	490	6
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr12:25398284C>T	ENST00000311936.3	-	2	226	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000256078.4_Missense_Mutation_p.G12D	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>A	12.37:g.25398284C>T	ENSP00000308495:p.Gly12Asp	NA	A8K8Z5|B0LPF9|P01118|Q96D10	37	CCDS8702.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	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 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	94	14
KRT5	3852	broad.mit.edu	37	12	52910448	52910448	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr12:52910448C>T	ENST00000252242.4	-	7	1802	c.1412G>A	c.(1411-1413)cGc>cAc	p.R471H		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	471	Coil 2.|Rod.				epidermis development|hemidesmosome assembly	cytosol|keratin filament	protein binding|structural constituent of cytoskeleton			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		CAGCAGCTTGCGGTAAGTGGC	0.582		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													123	110	114			NA	NA	12		NA											NA				52910448		2203	4300	6503	SO:0001583	missense				CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081	3852	3852		-, Intermediate filaments type II, keratins (basic)	6442	protein-coding gene	gene with protein product		148040	epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types, keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)	EBS2	NA	1713141, 16831889	Standard		NM_000424	NA	Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.1412G>A	12.37:g.52910448C>T	ENSP00000252242:p.Arg471His	NA	Q6PI71|Q6UBJ0|Q8TA91	37	CCDS8830.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.959666	0.92791	.	.	ENSG00000186081	ENST00000252242;ENST00000456000	D	0.94687	-3.49	5.93	5.93	0.95920	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.52532	D	0.000069	D	0.97977	0.9334	H	0.95224	3.64	0.46044	D	0.998833	D	0.89917	1.0	D	0.80764	0.994	D	0.98525	1.0625	10	0.87932	D	0	.	13.5241	0.61584	0.0:0.9291:0.0:0.0709	.	471	P13647	K2C5_HUMAN	H	471;436	ENSP00000252242:R471H	ENSP00000252242:R471H	R	-	2	0	KRT5	51196715	0.995000	0.38212	0.563000	0.28383	0.926000	0.56050	7.743000	0.85020	2.805000	0.96524	0.655000	0.94253	CGC	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000405312.1		-	ENST00000252242.4	Missense_Mutation	SNP	12 : 52910448 - 52910448 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	441	5
LCN9	392399	broad.mit.edu	37	9	138557549	138557549	+	Silent	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr9:138557549C>T	ENST00000277526.3	+	5	426	c.426C>T	c.(424-426)tgC>tgT	p.C142C	LCN9_ENST00000430290.2_3'UTR	NM_001001676.1	NP_001001676.1	Q8WX39	LCN9_HUMAN	lipocalin 9	142						extracellular region	pheromone binding|transporter activity			kidney(1)|large_intestine(2)|lung(2)|urinary_tract(1)	6		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;3.43e-07)|Epithelial(140;1.97e-06)|all cancers(34;6.1e-05)		AAGAAACCTGCGAAAAGTACG	0.572		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													44	44	44			NA	NA	9		NA											NA				138557549		1925	4121	6046	SO:0001819	synonymous_variant			AY301270	CCDS56593.1	9q34	2011-11-14			ENSG00000148386	ENSG00000148386	392399	392399		Lipocalins	17442	protein-coding gene	gene with protein product	MUP-like lipocalin, epididymal-specific lipocalin-9	612903			NA	15363845	Standard	NM_001001676	NM_001001676	NA	Approved		uc004cgk.2	Q8WX39	OTTHUMG00000020916	ENST00000277526.3:c.426C>T	9.37:g.138557549C>T		NA	C9J5F0|Q6JVE7	37	CCDS56593.1																																																																																			LCN9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410711.1		+	ENST00000277526.3	Silent	SNP	9 : 138557549 - 138557549 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	91	18
LRIG3	121227	broad.mit.edu	37	12	59277344	59277344	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	A	A	-	-	A	A	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr12:59277344delA	ENST00000320743.3	-	11	1560	c.1274delT	c.(1273-1275)ttafs	p.L425fs	LRIG3_ENST00000379141.4_Frame_Shift_Del_p.L365fs	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	425						integral to membrane			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			ATTGCCTTGTAAAGACATGAT	0.383		NA	T	ROS1	NSCLC									NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA				Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	0													122	116	118			NA	NA	12		NA											NA				59277344		2203	4300	6503	SO:0001589	frameshift_variant			AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263	121227	121227		Immunoglobulin superfamily / I-set domain containing	30991	protein-coding gene	gene with protein product		608870			NA		Standard	NM_153377	NM_153377	NA	Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.1274delT	12.37:g.59277344delA	ENSP00000326759:p.Leu425fs	NA	Q6UXL7|Q8NC72	37	CCDS8960.1																																																																																			LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406623.1		-	ENST00000320743.3	Frame_Shift_Del	DEL	12 : 59277344 - 59277344 - PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	203	40
LRIT1	26103	broad.mit.edu	37	10	85991943	85991943	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr10:85991943C>T	ENST00000372105.3	-	4	1633	c.1612G>A	c.(1612-1614)Gtc>Atc	p.V538I		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	538						integral to endoplasmic reticulum membrane		p.V538I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						AGGGCAATGACGATGGCCACA	0.532		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)											112	88	96			NA	NA	10		NA											NA				85991943		2203	4300	6503	SO:0001583	missense			AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602	26103	26103		Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	23404	protein-coding gene	gene with protein product	fibronectin type III, immunoglobulin and leucine rich repeat domains 9		leucine rich repeat containing 21	LRRC21	NA	10777785	Standard	NM_015613	NM_015613	NA	Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.1612G>A	10.37:g.85991943C>T	ENSP00000361177:p.Val538Ile	NA	Q9Y4N7	37	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	C	9.192	1.026386	0.19512	.	.	ENSG00000148602	ENST00000372105	T	0.42513	0.97	5.62	2.5	0.30297	.	0.565141	0.18543	N	0.138159	T	0.24044	0.0582	L	0.41632	1.29	0.42532	D	0.993043	P	0.36633	0.562	B	0.29862	0.108	T	0.07770	-1.0755	10	0.07030	T	0.85	.	7.4198	0.27065	0.0:0.6491:0.0:0.3509	.	538	Q9P2V4	LRIT1_HUMAN	I	538	ENSP00000361177:V538I	ENSP00000361177:V538I	V	-	1	0	LRIT1	85981923	0.981000	0.34729	0.410000	0.26471	0.092000	0.18411	2.499000	0.45372	0.580000	0.29522	0.563000	0.77884	GTC	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049109.1		-	ENST00000372105.3	Missense_Mutation	SNP	10 : 85991943 - 85991943 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	231	36
LSR	51599	broad.mit.edu	37	19	35753550	35753550	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr19:35753550G>A	ENST00000602122.1	+	4	1307	c.820G>A	c.(820-822)Gtc>Atc	p.V274I	LSR_ENST00000597933.1_3'UTR|LSR_ENST00000354900.3_Missense_Mutation_p.V274I|LSR_ENST00000347609.4_Missense_Mutation_p.V256I|LSR_ENST00000360798.3_Intron|LSR_ENST00000427250.1_Intron|LSR_ENST00000361790.3_Missense_Mutation_p.V293I			Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	293					embryo development|liver development	chylomicron|integral to membrane|low-density lipoprotein particle|plasma membrane|very-low-density lipoprotein particle	receptor activity			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CTGCTGCTACGTCAGGTGCCC	0.627		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													100	80	87			NA	NA	19		NA											NA				35753550		2203	4300	6503	SO:0001583	missense			AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699	51599	51599		Immunoglobulin superfamily / Immunoglobulin-like domain containing	29572	protein-coding gene	gene with protein product	lipolysis-stimulated remnant, immunoglobulin-like domain containing receptor 3				NA	10224102	Standard	NM_015925	NM_015925	NA	Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000602122.1:c.820G>A	19.37:g.35753550G>A	ENSP00000472569:p.Val274Ile	NA	O00112|O00426|Q6ZT80|Q9UQL3	37	CCDS59376.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862120	0.71949	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000347609	T;T;T	0.57107	0.42;0.42;0.42	4.74	4.74	0.60224	LISCH7 (1);	0.065915	0.64402	D	0.000014	T	0.57286	0.2043	L	0.34521	1.04	0.80722	D	1	D;D;D;P	0.76494	0.999;0.977;0.982;0.84	P;P;P;B	0.61070	0.883;0.525;0.562;0.344	T	0.52155	-0.8613	10	0.27785	T	0.31	-37.3992	15.256	0.73585	0.0:0.0:1.0:0.0	.	256;274;274;293	Q86X29-2;Q86X29-3;E9PHD4;Q86X29	.;.;.;LSR_HUMAN	I	293;274;256	ENSP00000354575:V293I;ENSP00000346976:V274I;ENSP00000262627:V256I	ENSP00000262627:V256I	V	+	1	0	LSR	40445390	1.000000	0.71417	0.946000	0.38457	0.967000	0.64934	4.937000	0.63513	2.448000	0.82819	0.591000	0.81541	GTC	LSR-001	KNOWN	NAGNAG_splice_site|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465221.3		+	ENST00000602122.1	Missense_Mutation	SNP	19 : 35753550 - 35753550 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	480	82
LTBP4	8425	broad.mit.edu	37	19	41123123	41123123	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr19:41123123C>G	ENST00000602240.1	+	0	3152				LTBP4_ENST00000243562.9_Missense_Mutation_p.H141Q|LTBP4_ENST00000545697.1_Intron|LTBP4_ENST00000396819.3_Missense_Mutation_p.H1020Q|LTBP4_ENST00000204005.9_Missense_Mutation_p.H1050Q|LTBP4_ENST00000308370.7_Missense_Mutation_p.H1087Q			Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding protein 4	NA					growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)			ATGGGCGTCACTGCGTGGGTA	0.622		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													26	27	27			NA	NA	19		NA											NA				41123123		1980	4153	6133	SO:0001624	3_prime_UTR_variant			Y13622	CCDS74368.1, CCDS74369.1, CCDS74370.1	19q13.1-q13.2	2011-10-20				ENSG00000090006	8425	8425		Latent transforming growth factor, beta binding proteins	6717	protein-coding gene	gene with protein product		604710			NA	9660815, 9271198	Standard	NM_003573	NM_003573	NA	Approved	LTBP-4, LTBP-4L, FLJ46318, FLJ90018	uc002ooh.1	Q8N2S1		ENST00000602240.1:c.*3149C>G	19.37:g.41123123C>G		NA	O00508|O75412|O75413	37		.	.	.	.	.	.	.	.	.	.	C	16.00	2.999789	0.54147	.	.	ENSG00000090006	ENST00000204005;ENST00000308370;ENST00000396819;ENST00000243562	D;D;D;D	0.91631	-2.19;-2.88;-2.19;-2.88	4.19	4.19	0.49359	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.42420	D	0.000715	D	0.94138	0.8120	.	.	.	0.80722	D	1	D;D;D	0.89917	0.995;1.0;1.0	D;D;D	0.87578	0.993;0.998;0.998	D	0.91644	0.5329	9	0.13470	T	0.59	.	15.8101	0.78552	0.0:1.0:0.0:0.0	.	1020;1088;1050	E7EUU1;Q8N2S1;E7ENG9	.;LTBP4_HUMAN;.	Q	1050;1087;1020;141	ENSP00000204005:H1050Q;ENSP00000311905:H1087Q;ENSP00000380031:H1020Q;ENSP00000243562:H141Q	ENSP00000204005:H1050Q	H	+	3	2	LTBP4	45814963	0.611000	0.26992	1.000000	0.80357	0.994000	0.84299	-0.142000	0.10311	2.330000	0.79161	0.563000	0.77884	CAC	LTBP4-002	KNOWN	sequence_error|basic	processed_transcript	NA	protein_coding	OTTHUMT00000462815.2		+	ENST00000602240.1	3'UTR	SNP	19 : 41123123 - 41123123 G PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	201	26
LZTS3	0	broad.mit.edu	37	20	3145122	3145122	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr20:3145122C>T	ENST00000329152.3	-	3	3397	c.2000G>A	c.(1999-2001)cGc>cAc	p.R667H	LZTS3_ENST00000360342.3_Missense_Mutation_p.R621H|LZTS3_ENST00000337576.5_Missense_Mutation_p.R621H						NA											NA						GGACTCAATGCGCTCGAGGCG	0.647		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													57	59	58			NA	NA	20		NA											NA				3145122		2203	4300	6503	SO:0001583	missense											NA	NA			NA							NA					NA						ENST00000329152.3:c.2000G>A	20.37:g.3145122C>T	ENSP00000332123:p.Arg667His	NA		37	CCDS13049.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.274509	0.80580	.	.	ENSG00000088899	ENST00000329152;ENST00000360342;ENST00000337576	T;T;T	0.43294	0.95;1.09;1.09	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.52092	0.1713	L	0.27053	0.805	0.52099	D	0.999942	D;D	0.89917	1.0;0.998	D;D	0.69479	0.96;0.964	T	0.57768	-0.7754	10	0.72032	D	0.01	-15.1298	17.8165	0.88635	0.0:1.0:0.0:0.0	.	621;667	O60299-2;O60299	.;PRIP1_HUMAN	H	667;621;621	ENSP00000332123:R667H;ENSP00000353496:R621H;ENSP00000338166:R621H	ENSP00000332123:R667H	R	-	2	0	RP5-1187M17.10	3093122	0.975000	0.34042	1.000000	0.80357	0.961000	0.63080	2.377000	0.44300	2.442000	0.82660	0.555000	0.69702	CGC	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077715.2		-	ENST00000329152.3	Missense_Mutation	SNP	20 : 3145122 - 3145122 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	434	5
MC5R	4161	broad.mit.edu	37	18	13826098	13826098	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr18:13826098C>T	ENST00000324750.3	+	1	556	c.334C>T	c.(334-336)Cgc>Tgc	p.R112C		NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	112					G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocortin receptor activity|protein binding			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|upper_aerodigestive_tract(1)	41						CGCCTTTGTGCGCCACATTGA	0.522		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													152	124	133			NA	NA	18		NA											NA				13826098		2203	4300	6503	SO:0001583	missense			AY268429	CCDS11868.1	18p11.2	2012-08-10			ENSG00000176136	ENSG00000176136	4161	4161		GPCR / Class A : Melanocortin receptors	6933	protein-coding gene	gene with protein product		600042			NA	8396929	Standard	NM_005913	NM_005913	NA	Approved		uc010xaf.2	P33032	OTTHUMG00000131720	ENST00000324750.3:c.334C>T	18.37:g.13826098C>T	ENSP00000318077:p.Arg112Cys	NA	B0YJ34|Q502V1	37	CCDS11868.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.704257	0.48412	.	.	ENSG00000176136	ENST00000324750	T	0.20738	2.05	4.9	3.1	0.35709	GPCR, rhodopsin-like superfamily (1);	0.103679	0.64402	D	0.000005	T	0.33789	0.0875	L	0.39898	1.24	0.58432	D	0.999999	D	0.89917	1.0	D	0.70716	0.97	T	0.02909	-1.1095	10	0.87932	D	0	.	10.9647	0.47406	0.1464:0.7129:0.1407:0.0	.	112	P33032	MC5R_HUMAN	C	112	ENSP00000318077:R112C	ENSP00000318077:R112C	R	+	1	0	MC5R	13816098	1.000000	0.71417	0.932000	0.37286	0.749000	0.42624	2.825000	0.48096	0.467000	0.27218	-0.384000	0.06662	CGC	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254638.1		+	ENST00000324750.3	Missense_Mutation	SNP	18 : 13826098 - 13826098 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	136	65
NARG2	0	broad.mit.edu	37	15	60747571	60747571	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	A	A	-	-	A	A	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr15:60747571A>G	ENST00000261520.4	-	7	971	c.737T>C	c.(736-738)aTa>aCa	p.I246T	NARG2_ENST00000561114.1_Missense_Mutation_p.I246T|NARG2_ENST00000439632.1_Missense_Mutation_p.I109T	NM_024611.4	NP_078887.2	Q659A1	NARG2_HUMAN		246						nucleus				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						AATGGTAGCTATATCGTCCTT	0.333		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													199	181	187			NA	NA	15		NA											NA				60747571		2202	4300	6502	SO:0001583	missense											NA	NA			NA							NA					NA						ENST00000261520.4:c.737T>C	15.37:g.60747571A>G	ENSP00000261520:p.Ile246Thr	NA	B2RU08|Q05CT1|Q3B7W6|Q63HP4|Q658Q0|Q68CN8|Q6IPW7|Q6UX23|Q71H65|Q96CY5|Q9HAA2	37	CCDS10176.1	.	.	.	.	.	.	.	.	.	.	A	1.299	-0.605421	0.03717	.	.	ENSG00000128915	ENST00000261520;ENST00000439632	.	.	.	4.68	-1.88	0.07713	.	0.620823	0.16985	N	0.191552	T	0.16599	0.0399	N	0.16478	0.41	0.09310	N	1	B;B	0.10296	0.0;0.003	B;B	0.09377	0.0;0.004	T	0.12016	-1.0564	9	0.32370	T	0.25	-0.2145	4.7993	0.13289	0.6043:0.0:0.211:0.1848	.	109;246	G3V0H6;Q659A1	.;NARG2_HUMAN	T	246;109	.	ENSP00000261520:I246T	I	-	2	0	NARG2	58534863	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.076000	0.14712	-0.078000	0.12730	-0.313000	0.08912	ATA	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256136.1		-	ENST00000261520.4	Missense_Mutation	SNP	15 : 60747571 - 60747571 G PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	372	91
NEUROD6	63974	broad.mit.edu	37	7	31377972	31377972	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr7:31377972G>A	ENST00000297142.3	-	2	1233	c.911C>T	c.(910-912)gCc>gTc	p.A304V		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	304					cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						CCTGAACATGGCACCCTGCCC	0.468		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													90	89	90			NA	NA	7		NA											NA				31377972		2203	4300	6503	SO:0001583	missense			AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600	63974	63974		Basic helix-loop-helix proteins	13804	protein-coding gene	gene with protein product		611513	neurogenic differentiation 6		NA	12357074	Standard	NM_022728	NM_022728	NA	Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.911C>T	7.37:g.31377972G>A	ENSP00000297142:p.Ala304Val	NA	Q9H3H6	37	CCDS5434.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629527	0.46944	.	.	ENSG00000164600	ENST00000297142	D	0.95238	-3.65	5.13	5.13	0.70059	.	0.108251	0.64402	D	0.000004	D	0.89181	0.6642	L	0.27053	0.805	0.50813	D	0.999898	B	0.16396	0.017	B	0.18263	0.021	D	0.84308	0.0509	10	0.02654	T	1	-19.6987	18.5931	0.91222	0.0:0.0:1.0:0.0	.	304	Q96NK8	NDF6_HUMAN	V	304	ENSP00000297142:A304V	ENSP00000297142:A304V	A	-	2	0	NEUROD6	31344497	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.414000	0.97362	2.386000	0.81285	0.650000	0.86243	GCC	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215050.1		-	ENST00000297142.3	Missense_Mutation	SNP	7 : 31377972 - 31377972 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	234	5
NOS1	4842	broad.mit.edu	37	12	117662845	117662845	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr12:117662845G>A	ENST00000338101.4	-	25	3908	c.3904C>T	c.(3904-3906)Cgg>Tgg	p.R1302W	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.R1268W			P29475	NOS1_HUMAN	nitric oxide synthase 1 (neuronal)	1268					multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	TCAAATTGCCGCTGTTGCCAG	0.612		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA		Esophageal Squamous(162;1748 2599 51982 52956)							NA				0													146	159	155			NA	NA	12		NA											NA				117662845		1948	4149	6097	SO:0001583	missense				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	4842	4842	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS	NA	1385308, 7682706	Standard		NM_001204213	NA	Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.3904C>T	12.37:g.117662845G>A	ENSP00000337459:p.Arg1302Trp	NA		37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.874204	0.72180	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000338101	D;D	0.85258	-1.96;-1.96	4.93	4.0	0.46444	Oxidoreductase FAD/NAD(P)-binding (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	0.000000	0.85682	D	0.000000	D	0.93680	0.7981	M	0.93594	3.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94520	0.7726	10	0.66056	D	0.02	-31.3949	13.4871	0.61373	0.0:0.0:0.731:0.269	.	1268	P29475	NOS1_HUMAN	W	1163;1268;1302	ENSP00000320758:R1268W;ENSP00000337459:R1302W	ENSP00000320758:R1268W	R	-	1	2	NOS1	116147228	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	2.995000	0.49441	2.555000	0.86185	0.561000	0.74099	CGG	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268053.1		-	ENST00000338101.4	Missense_Mutation	SNP	12 : 117662845 - 117662845 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	636	209
NUP62	23636	broad.mit.edu	37	19	50412865	50412865	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr19:50412865G>A	ENST00000596217.1	-	2	2087	c.200C>T	c.(199-201)cCg>cTg	p.P67L	NUP62_ENST00000597029.1_Missense_Mutation_p.P67L|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000352066.3_Missense_Mutation_p.P67L|NUP62_ENST00000413454.1_Missense_Mutation_p.P67L|NUP62_ENST00000422090.2_Missense_Mutation_p.P67L|CTC-326K19.6_ENST00000451973.1_3'UTR|NUP62_ENST00000597723.1_Missense_Mutation_p.P67L|IL4I1_ENST00000341114.3_Intron			P37198	NUP62_HUMAN	nucleoporin 62kDa	67	15 X 9 AA approximate repeats.|Thr-rich.				carbohydrate metabolic process|cell death|cell surface receptor linked signaling pathway|glucose transport|hormone-mediated signaling pathway|mRNA transport|negative regulation of apoptosis|negative regulation of cell proliferation|nucleocytoplasmic transport|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription, DNA-dependent|protein transport|regulation of glucose transport|transcription, DNA-dependent|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleocytoplasmic shuttling complex|ribonucleoprotein complex|spindle pole	chromatin binding|protein serine/threonine kinase activity|receptor signaling complex scaffold activity|SH2 domain binding|structural constituent of nuclear pore|thyroid hormone receptor binding|ubiquitin binding			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		CTGTGTGGCCGGAGTCTGGGT	0.552		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													150	154	153			NA	NA	19		NA											NA				50412865		2203	4300	6503	SO:0001583	missense			X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024	23636	23636			8066	protein-coding gene	gene with protein product	nuclear pore glycoprotein p62	605815	nucleoporin 62kD		NA	1915414	Standard	NM_153719	NM_016553	NA	Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.200C>T	19.37:g.50412865G>A	ENSP00000471191:p.Pro67Leu	NA	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	37	CCDS12788.1	.	.	.	.	.	.	.	.	.	.	G	11.83	1.755489	0.31046	.	.	ENSG00000213024	ENST00000319225;ENST00000352066;ENST00000422090;ENST00000413454	T;T;T	0.38722	1.12;1.12;1.12	4.16	3.12	0.35913	Nucleoporin, NSP1-like, C-terminal (1);	0.403038	0.21678	U	0.070777	T	0.29716	0.0742	L	0.38531	1.155	0.42109	D	0.991379	P;P	0.47545	0.89;0.897	B;B	0.39419	0.299;0.157	T	0.13683	-1.0500	10	0.72032	D	0.01	-4.6212	7.9938	0.30256	0.1097:0.0:0.8903:0.0	.	67;67	Q8WYU3;P37198	.;NUP62_HUMAN	L	67	ENSP00000305503:P67L;ENSP00000407331:P67L;ENSP00000387991:P67L	ENSP00000321866:P67L	P	-	2	0	NUP62	55104677	0.914000	0.31030	0.018000	0.16275	0.019000	0.09904	6.760000	0.74939	1.339000	0.45563	0.655000	0.94253	CCG	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464991.1		-	ENST00000596217.1	Missense_Mutation	SNP	19 : 50412865 - 50412865 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	610	6
OR2G6	391211	broad.mit.edu	37	1	248685733	248685733	+	Silent	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr1:248685733G>A	ENST00000343414.4	+	1	818	c.786G>A	c.(784-786)ccG>ccA	p.P262P		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	262					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACCTTCAACCGGCCAATAGGA	0.448		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													109	111	110			NA	NA	1		NA											NA				248685733		2203	4300	6503	SO:0001819	synonymous_variant				CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558	391211	391211		GPCR / Class A : Olfactory receptors	27019	protein-coding gene	gene with protein product					NA		Standard	XM_372842	NM_001013355	NA	Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.786G>A	1.37:g.248685733G>A		NA	B2RP33	37	CCDS31119.1																																																																																			OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000097358.1		+	ENST00000343414.4	Silent	SNP	1 : 248685733 - 248685733 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	283	5
OR2Z1	284383	broad.mit.edu	37	19	8841649	8841649	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr19:8841649C>T	ENST00000324060.2	+	1	334	c.259C>T	c.(259-261)Cgg>Tgg	p.R87W		NM_001004699.1	NP_001004699.1	Q8NG97	OR2Z1_HUMAN	olfactory receptor, family 2, subfamily Z, member 1	87					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						AGACTTTCTGCGGGGAGAAGG	0.552		NA											C	1	5e-04	NA	0.0028	2184	NA	1	,	,	NA	3e-04	NA	NA	NA	5e-04	1	EXOME	NA	NA	4e-04	SNP								NA				0								C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	108	95	100		259	3	0	19		100	0,8600		0,0,4300	no	missense	OR2Z1	NM_001004699.1	101	0,1,6502	TT,TC,CC	NA	0.0,0.0227,0.0077	benign	87/315	8841649	1,13005	2203	4300	6503	SO:0001583	missense			AC008753	CCDS32895.1	19p13.2	2013-09-20	2002-11-13		ENSG00000181733	ENSG00000181733	284383	284383		GPCR / Class A : Olfactory receptors	15391	protein-coding gene	gene with protein product			olfactory receptor, family 2, subfamily Z, member 2	OR2Z2	NA		Standard		NM_001004699	NA	Approved		uc010xkg.2	Q8NG97	OTTHUMG00000182195	ENST00000324060.2:c.259C>T	19.37:g.8841649C>T	ENSP00000316284:p.Arg87Trp	NA	B9EH50|Q6IFK0|Q96R25	37	CCDS32895.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	2.412	-0.335123	0.05278	2.27E-4	0.0	ENSG00000181733	ENST00000324060	T	0.00406	7.55	4.33	3.05	0.35203	GPCR, rhodopsin-like superfamily (1);	2.610920	0.01162	N	0.006663	T	0.00384	0.0012	L	0.39514	1.22	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.49606	-0.8922	10	0.38643	T	0.18	.	7.9281	0.29887	0.0:0.8369:0.0:0.1631	.	87	Q8NG97	OR2Z1_HUMAN	W	87	ENSP00000316284:R87W	ENSP00000316284:R87W	R	+	1	2	OR2Z1	8702649	0.000000	0.05858	0.009000	0.14445	0.011000	0.07611	-0.537000	0.06128	2.182000	0.69389	0.543000	0.68304	CGG	OR2Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459954.1		+	ENST00000324060.2	Missense_Mutation	SNP	19 : 8841649 - 8841649 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	539	5
PCDH1	5097	broad.mit.edu	37	5	141243880	141243880	+	Silent	SNP	G	G	A	rs149691852	by1000genomes	TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr5:141243880G>A	ENST00000287008.3	-	3	2163	c.2016C>T	c.(2014-2016)agC>agT	p.S672S	PCDH1_ENST00000503492.1_Intron|PCDH1_ENST00000456271.1_Silent_p.S660S|PCDH1_ENST00000511044.1_5'UTR|PCDH1_ENST00000536585.1_Silent_p.S650S|PCDH1_ENST00000394536.3_Silent_p.S672S	NM_032420.2	NP_115796.2	Q08174	PCDH1_HUMAN	protocadherin 1	672	Cadherin 6.				cell-cell signaling|homophilic cell adhesion|nervous system development	cell-cell junction|integral to plasma membrane	calcium ion binding			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		CTCGATCAAAGCTCAGGCTGG	0.552		NA											g	1	5e-04	NA	NA	2184	NA	1	,	,	NA	3e-04	0.0013	NA	NA	5e-04	1	LOWCOV,EXOME	NA	NA	0.0011	SNP	Ovarian(132;1609 1739 4190 14731 45037)							NA				0													130	127	128			NA	NA	5		NA											NA				141243880		2203	4300	6503	SO:0001819	synonymous_variant			AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453	5097	5097		Cadherins / Protocadherins : Non-clustered	8655	protein-coding gene	gene with protein product		603626	protocadherin 1 (cadherin-like 1)		NA	8508762	Standard	NM_032420	NM_032420	NA	Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000287008.3:c.2016C>T	5.37:g.141243880G>A		NA	Q8IUP2	37	CCDS4267.1																																																																																			PCDH1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320587.2		-	ENST00000287008.3	Silent	SNP	5 : 141243880 - 141243880 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	354	82
PCDHA4	56144	broad.mit.edu	37	5	140188813	140188813	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr5:140188813C>T	ENST00000530339.1	+	1	2041	c.2041C>T	c.(2041-2043)Cgg>Tgg	p.R681W	PCDHA4_ENST00000512229.2_Missense_Mutation_p.R681W|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.R681W	NM_018907.2	NP_061730.1			protocadherin alpha 4	NA										breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCCTCCTCACGGGCGTTGGT	0.632		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													57	57	57			NA	NA	5		NA											NA				140188813		2203	4300	6503	SO:0001583	missense			AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967	56144	56144		Cadherins / Protocadherins : Clustered	8670	other	complex locus constituent	ortholog of mouse CNR1, KIAA0345-like 10	606310			NA	10380929, 10662547	Standard	NM_018907	NM_018907	NA	Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.2041C>T	5.37:g.140188813C>T	ENSP00000435300:p.Arg681Trp	NA		37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	c	11.80	1.746491	0.30955	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.54071	0.63;0.59;0.6	3.93	-0.744	0.11101	.	0.210729	0.23351	U	0.049123	T	0.51466	0.1676	M	0.89601	3.045	0.09310	N	1	B;B;B	0.32717	0.381;0.082;0.137	B;B;B	0.32289	0.143;0.022;0.022	T	0.52366	-0.8585	10	0.66056	D	0.02	.	4.0101	0.09619	0.4068:0.383:0.1322:0.078	.	681;681;681	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	W	681	ENSP00000423470:R681W;ENSP00000349344:R681W;ENSP00000435300:R681W	ENSP00000349344:R681W	R	+	1	2	PCDHA4	140168997	0.171000	0.23029	0.001000	0.08648	0.014000	0.08584	0.000000	0.12993	-0.051000	0.13334	-0.516000	0.04426	CGG	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372864.2		+	ENST00000530339.1	Missense_Mutation	SNP	5 : 140188813 - 140188813 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	316	61
PCDHGA12	26025	broad.mit.edu	37	5	140810888	140810888	+	Missense_Mutation	SNP	G	G	A	rs112186927	byFrequency	TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr5:140810888G>A	ENST00000252085.3	+	1	704	c.562G>A	c.(562-564)Ggt>Agt	p.G188S	PCDHGB1_ENST00000523390.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1			protocadherin gamma subfamily A, 12	NA										breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGAGCCGACGGTAGTAAGTA	0.607		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													92	99	96			NA	NA	5		NA											NA				140810888		2203	4300	6503	SO:0001583	missense			AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159	26025	26025		Cadherins / Protocadherins : Clustered	8699	other	protocadherin	fibroblast cadherin FIB3	603059	cadherin 21	CDH21	NA	10380929	Standard	NM_003735	NM_003735	NA	Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.562G>A	5.37:g.140810888G>A	ENSP00000252085:p.Gly188Ser	NA		37	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	g	15.60	2.882516	0.51908	.	.	ENSG00000253159	ENST00000252085	T	0.20332	2.08	5.8	5.8	0.92144	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.57080	0.2029	M	0.93375	3.41	0.30472	N	0.773188	D;D	0.65815	0.993;0.995	P;P	0.60473	0.766;0.875	T	0.65899	-0.6056	9	0.59425	D	0.04	.	19.6649	0.95889	0.0:0.0:1.0:0.0	.	188;188	O60330-2;O60330	.;PCDGC_HUMAN	S	188	ENSP00000252085:G188S	ENSP00000252085:G188S	G	+	1	0	PCDHGA12	140791072	1.000000	0.71417	0.311000	0.25182	0.004000	0.04260	2.963000	0.49184	2.748000	0.94277	0.655000	0.94253	GGT	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251806.2		+	ENST00000252085.3	Missense_Mutation	SNP	5 : 140810888 - 140810888 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	639	128
PIK3CB	5291	broad.mit.edu	37	3	138382857	138382857	+	Missense_Mutation	SNP	C	C	T	rs142933486	by1000genomes	TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr3:138382857C>T	ENST00000477593.1	-	20	2760	c.2687G>A	c.(2686-2688)cGa>cAa	p.R896Q	PIK3CB_ENST00000289153.2_Missense_Mutation_p.R896Q|PIK3CB_ENST00000544716.1_Missense_Mutation_p.R347Q			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	896	PI3K/PI4K.				activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						CTCAATGGCTCGGTCCAGGTC	0.448		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													80	71	74			NA	NA	3		NA											NA				138382857		2203	4300	6503	SO:0001583	missense				CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	5291	5291	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	phosphoinositide-3-kinase, catalytic, beta polypeptide	PIK3C1	NA	8246984	Standard		NM_006219	NA	Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.2687G>A	3.37:g.138382857C>T	ENSP00000418143:p.Arg896Gln	NA	D3DNF0|Q24JU2	37	CCDS3104.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.04|17.04	3.286996|3.286996	0.59867|0.59867	.|.	.|.	ENSG00000051382|ENSG00000051382	ENST00000493568|ENST00000477593;ENST00000544716;ENST00000289153	.|T;T;T	.|0.76060	.|-0.99;-0.99;-0.99	5.63|5.63	5.63|5.63	0.86233|0.86233	.|Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.63640|0.63640	0.2528|0.2528	L|L	0.31207|0.31207	0.915|0.915	0.58432|0.58432	D|D	0.999998|0.999998	.|B;B;B	.|0.33379	.|0.269;0.178;0.41	.|B;B;B	.|0.24541	.|0.041;0.044;0.054	T|T	0.60662|0.60662	-0.7219|-0.7219	5|10	.|0.28530	.|T	.|0.3	-11.8261|-11.8261	20.0442|20.0442	0.97604|0.97604	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|896;483;347	.|P42338;B4DZI3;Q68DL0	.|PK3CB_HUMAN;.;.	K|Q	528|896;347;896	.|ENSP00000418143:R896Q;ENSP00000438259:R347Q;ENSP00000289153:R896Q	.|ENSP00000289153:R896Q	E|R	-|-	1|2	0|0	PIK3CB|PIK3CB	139865547|139865547	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.138000|3.138000	0.50570|0.50570	2.814000|2.814000	0.96858|0.96858	0.655000|0.655000	0.94253|0.94253	GAG|CGA	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358019.1		-	ENST00000477593.1	Missense_Mutation	SNP	3 : 138382857 - 138382857 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	147	31
PYROXD2	84795	broad.mit.edu	37	10	100155147	100155147	+	Splice_Site	SNP	C	C	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr10:100155147C>A	ENST00000370575.4	-	7	736		c.e7+1		PYROXD2_ENST00000483923.1_Splice_Site	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	NA							oxidoreductase activity			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						GAACCACTCACCTTGGTAATG	0.577		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													152	155	154			NA	NA	10		NA											NA				100155147		2203	4300	6503	SO:0001630	splice_region_variant			AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943	84795	84795			23517	protein-coding gene	gene with protein product			chromosome 10 open reading frame 33	C10orf33	NA		Standard	NM_032709	NM_032709	NA	Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.687+1G>T	10.37:g.100155147C>A		NA	D3DR61|Q5TAA9|Q9BRQ1	37	CCDS7474.1	.	.	.	.	.	.	.	.	.	.	C	18.58	3.654104	0.67472	.	.	ENSG00000119943	ENST00000370575	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4032	0.87466	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PYROXD2	100145137	1.000000	0.71417	0.993000	0.49108	0.817000	0.46193	3.922000	0.56462	2.386000	0.81285	0.655000	0.94253	.	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049782.2	Intron	-	ENST00000370575.4	Splice_Site	SNP	10 : 100155147 - 100155147 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	858	7
RANBP2	5903	broad.mit.edu	37	2	109371498	109371498	+	Silent	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr2:109371498G>A	ENST00000283195.6	+	16	2466	c.2340G>A	c.(2338-2340)ccG>ccA	p.P780P		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	780					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						ATTCTACACCGTCTCCTACCA	0.353		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													98	103	101			NA	NA	2		NA											NA				109371498		2198	4282	6480	SO:0001819	synonymous_variant			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201	5903	5903		Tetratricopeptide (TTC) repeat domain containing	9848	protein-coding gene	gene with protein product		601181	acute necrotizing encephalopathy 1 (autosomal dominant)	ANE1	NA	7724562, 19118815	Standard	NM_006267	NM_006267	NA	Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2340G>A	2.37:g.109371498G>A		NA	Q13074|Q15280|Q53TE2|Q59FH7	37	CCDS2079.1																																																																																			RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253594.1		+	ENST00000283195.6	Silent	SNP	2 : 109371498 - 109371498 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	563	6
RASGEF1C	255426	broad.mit.edu	37	5	179538479	179538479	+	Silent	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr5:179538479G>A	ENST00000393371.2	-	11	1577	c.1281C>T	c.(1279-1281)acC>acT	p.T427T	RASGEF1C_ENST00000522500.1_Silent_p.T276T|RASGEF1C_ENST00000361132.4_Silent_p.T427T			Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C	427	Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity			breast(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	12	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGATGGGGGCGGTGTACAGGT	0.592		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													136	93	108			NA	NA	5		NA											NA				179538479		2203	4300	6503	SO:0001819	synonymous_variant			AK093160	CCDS4452.1	5q35.3	2005-08-16			ENSG00000146090	ENSG00000146090	255426	255426			27400	protein-coding gene	gene with protein product					NA	12477932	Standard	NM_175062	XM_006714839	NA	Approved	FLJ35841	uc003mlr.3	Q8N431	OTTHUMG00000130914	ENST00000393371.2:c.1281C>T	5.37:g.179538479G>A		NA	D3DWQ7|Q7Z4T0|Q8NA49	37	CCDS4452.1																																																																																			RASGEF1C-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253506.2		-	ENST00000393371.2	Silent	SNP	5 : 179538479 - 179538479 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	224	47
RFPL1	5988	broad.mit.edu	37	22	29835118	29835118	+	Missense_Mutation	SNP	T	T	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	T	T	-	-	T	T	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr22:29835118T>A	ENST00000354373.2	+	1	547	c.338T>A	c.(337-339)aTt>aAt	p.I113N	RFPL1S_ENST00000461286.3_RNA	NM_021026.2	NP_066306.2	O75677	RFPL1_HUMAN	ret finger protein-like 1	113	B30.2/SPRY.						zinc ion binding			endometrium(3)|large_intestine(1)|lung(6)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	16						CTGAAGAAGATTCTGCAGATG	0.512		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	22		NA											NA				29835118		2203	4300	6503	SO:0001583	missense			AJ010228	CCDS13857.2	22q12	2006-04-25			ENSG00000128250	ENSG00000128250	5988	5988		RING-type (C3HC4) zinc fingers	9977	protein-coding gene	gene with protein product		605968			NA	10508838	Standard	NM_021026	NM_021026	NA	Approved	RNF78	uc003afn.3	O75677	OTTHUMG00000150516	ENST00000354373.2:c.338T>A	22.37:g.29835118T>A	ENSP00000346342:p.Ile113Asn	NA	Q6IC06|Q9UJ97	37	CCDS13857.2	.	.	.	.	.	.	.	.	.	.	-	12.72	2.023419	0.35701	.	.	ENSG00000128250	ENST00000354373	T	0.30448	1.53	1.66	-1.88	0.07713	RDM domain, Ret finger protein-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.37705	0.1013	L	0.52573	1.65	0.09310	N	1	D	0.59767	0.986	D	0.69307	0.963	T	0.24333	-1.0163	9	0.37606	T	0.19	.	2.2276	0.03988	0.0:0.235:0.315:0.45	.	113	O75677	RFPL1_HUMAN	N	113	ENSP00000346342:I113N	ENSP00000346342:I113N	I	+	2	0	RFPL1	28165118	0.004000	0.15560	0.004000	0.12327	0.209000	0.24338	-0.522000	0.06237	-0.097000	0.12307	0.342000	0.21767	ATT	RFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318719.1		+	ENST00000354373.2	Missense_Mutation	SNP	22 : 29835118 - 29835118 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	440	6
RUSC2	9853	broad.mit.edu	37	9	35555589	35555589	+	Missense_Mutation	SNP	T	T	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	T	T	-	-	T	T	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr9:35555589T>A	ENST00000455600.1	+	3	3116	c.2547T>A	c.(2545-2547)caT>caA	p.H849Q		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	849						cytosol				NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			ACCGGCTCCATGGAACAGGAA	0.647		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													46	45	46			NA	NA	9		NA											NA				35555589		2203	4300	6503	SO:0001583	missense			AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853	9853	9853			23625	protein-coding gene	gene with protein product		611053			NA	9205841	Standard	XM_048462	NM_001135999	NA	Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.2547T>A	9.37:g.35555589T>A	ENSP00000393922:p.His849Gln	NA	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	37	CCDS35008.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.328553	0.60743	.	.	ENSG00000198853	ENST00000361226;ENST00000455600;ENST00000543478	T;T	0.23348	1.91;1.91	4.15	4.15	0.48705	.	0.295723	0.38272	N	0.001756	T	0.25306	0.0615	L	0.29908	0.895	0.39729	D	0.971581	D	0.61697	0.99	P	0.50537	0.643	T	0.02901	-1.1096	10	0.37606	T	0.19	-8.6196	11.4069	0.49902	0.0:0.0:0.0:1.0	.	849	Q8N2Y8	RUSC2_HUMAN	Q	849	ENSP00000355177:H849Q;ENSP00000393922:H849Q	ENSP00000355177:H849Q	H	+	3	2	RUSC2	35545589	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.372000	0.44257	1.863000	0.54032	0.533000	0.62120	CAT	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052309.1		+	ENST00000455600.1	Missense_Mutation	SNP	9 : 35555589 - 35555589 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	383	97
SCNN1G	6340	broad.mit.edu	37	16	23226527	23226527	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr16:23226527C>T	ENST00000300061.2	+	13	1830	c.1687C>T	c.(1687-1689)Cgc>Tgc	p.R563C		NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	563					excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	TATCATTGCCCGCCGCCAGTG	0.587		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													95	88	90			NA	NA	16		NA											NA				23226527		2197	4300	6497	SO:0001583	missense			U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828	6340	6340		Ion channels / Sodium channel, nonvoltage-gated, Sodium channels	10602	protein-coding gene	gene with protein product		600761	sodium channel, nonvoltage-gated 1, gamma, sodium channel, non-voltage-gated 1, gamma		NA	7490094	Standard	NM_001039	NM_001039	NA	Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.1687C>T	16.37:g.23226527C>T	ENSP00000300061:p.Arg563Cys	NA	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	37	CCDS10608.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.801858	0.50315	.	.	ENSG00000166828	ENST00000300061	T	0.73258	-0.73	5.22	4.26	0.50523	.	0.000000	0.64402	D	0.000014	T	0.66790	0.2825	N	0.08118	0	0.51482	D	0.999928	D	0.89917	1.0	D	0.85130	0.997	T	0.67601	-0.5629	10	0.38643	T	0.18	-20.3075	9.9973	0.41907	0.1562:0.6932:0.1505:0.0	.	563	P51170	SCNNG_HUMAN	C	563	ENSP00000300061:R563C	ENSP00000300061:R563C	R	+	1	0	SCNN1G	23134028	1.000000	0.71417	0.466000	0.27168	0.654000	0.38779	2.845000	0.48254	1.154000	0.42482	0.561000	0.74099	CGC	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254496.1		+	ENST00000300061.2	Missense_Mutation	SNP	16 : 23226527 - 23226527 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	398	96
SEPHS2	22928	broad.mit.edu	37	16	30456111	30456111	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr16:30456111G>A	ENST00000478753.2	-	1	1391	c.938C>T	c.(937-939)gCg>gTg	p.A313V	SEPHS2_ENST00000500504.2_Missense_Mutation_p.A313V|SEPHS2_ENST00000542752.1_Missense_Mutation_p.A256V			Q99611	SPS2_HUMAN	selenophosphate synthetase 2	313					selenocysteine biosynthetic process		ATP binding|selenide, water dikinase activity			breast(3)|cervix(1)|kidney(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	10						ATCTGTGGCCGCATGGGCATT	0.448		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA		Esophageal Squamous(81;1142 1261 11202 24614 35697)							NA				0													98	91	93			NA	NA	16		NA											NA				30456111		1944	4143	6087	SO:0001583	missense			BC002381		16p11.2	2013-02-15			ENSG00000179918	ENSG00000179918	22928	22928			19686	protein-coding gene	gene with protein product		606218			NA	10608886	Standard	NM_012248	NM_012248	NA	Approved	SPS2, SPS2b	uc021tgl.1	Q99611	OTTHUMG00000176988	ENST00000478753.2:c.938C>T	16.37:g.30456111G>A	ENSP00000418669:p.Ala313Val	NA	Q9BUQ2	37		.	.	.	.	.	.	.	.	.	.	G	17.53	3.413384	0.62511	.	.	ENSG00000179918	ENST00000478753;ENST00000542752;ENST00000418751;ENST00000500504	T;T;T	0.64991	-0.13;-0.13;-0.13	5.28	5.28	0.74379	AIR synthase-related protein, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.76709	0.4025	H	0.94620	3.56	0.80722	D	1	P;P	0.49090	0.919;0.906	P;B	0.45343	0.477;0.2	D	0.84632	0.0690	10	0.87932	D	0	-10.0941	16.7892	0.85583	0.0:0.0:1.0:0.0	.	313;256	Q99611;F5H8F9	SPS2_HUMAN;.	V	313;256;264;313	ENSP00000418669:A313V;ENSP00000443601:A256V;ENSP00000426234:A313V	ENSP00000390233:A264V	A	-	2	0	SEPHS2	30363612	1.000000	0.71417	0.991000	0.47740	0.267000	0.26476	9.772000	0.98984	2.652000	0.90054	0.655000	0.94253	GCG	SEPHS2-001	KNOWN	basic|seleno	protein_coding	NA	protein_coding	OTTHUMT00000109640.11		-	ENST00000478753.2	Missense_Mutation	SNP	16 : 30456111 - 30456111 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	357	5
SGCZ	137868	broad.mit.edu	37	8	13947958	13947958	+	Nonsense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr8:13947958C>T	ENST00000382080.1	-	8	1648	c.933G>A	c.(931-933)tgG>tgA	p.W311*	SGCZ_ENST00000421524.2_Nonsense_Mutation_p.W264*	NM_139167.2	NP_631906.2	Q96LD1	SGCZ_HUMAN	sarcoglycan, zeta	298					cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				NS(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(14)|lung(15)|ovary(2)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	47				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		CACTTCAGCTCCACAGGCAGA	0.498		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													176	164	168			NA	NA	8		NA											NA				13947958		2203	4300	6503	SO:0001587	stop_gained			AY028700	CCDS5992.2	8p22	2014-09-17	2010-04-21		ENSG00000185053	ENSG00000185053	137868	137868			14075	protein-coding gene	gene with protein product		608113			NA	12189167	Standard	NM_139167	XM_006716287	NA	Approved	ZSG1	uc003wwq.3	Q96LD1	OTTHUMG00000090827	ENST00000382080.1:c.933G>A	8.37:g.13947958C>T	ENSP00000371512:p.Trp311*	NA	Q6REU0	37	CCDS5992.2	.	.	.	.	.	.	.	.	.	.	C	41	8.963007	0.99018	.	.	ENSG00000185053	ENST00000382080;ENST00000421524	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.39948	D	0.974498	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.7556	0.91832	0.0:1.0:0.0:0.0	.	.	.	.	X	311;264	.	ENSP00000371512:W311X	W	-	3	0	SGCZ	13992329	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.760000	0.94817	0.655000	0.94253	TGG	SGCZ-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207636.2		-	ENST00000382080.1	Nonsense_Mutation	SNP	8 : 13947958 - 13947958 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	460	85
SLC39A12	221074	broad.mit.edu	37	10	18292111	18292111	+	Missense_Mutation	SNP	G	G	A	rs142064736	byFrequency	TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr10:18292111G>A	ENST00000377371.3	+	12	1966	c.1768G>A	c.(1768-1770)Gtg>Atg	p.V590M	SLC39A12-AS1_ENST00000439319.1_RNA|SLC39A12-AS1_ENST00000445287.1_RNA|SLC39A12_ENST00000377374.4_Missense_Mutation_p.V554M|SLC39A12_ENST00000539911.1_Missense_Mutation_p.V457M|SLC39A12_ENST00000377369.2_Missense_Mutation_p.V591M			Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	591					zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						AGACTTTGCCGTGCTCTTAAG	0.393		NA											G	9	0.0041	0.02	0.0028	2184	NA	0.9999	,	,	NA	3e-04	NA	NA	NA	0.0042	0.9843	LOWCOV,EXOME	NA	NA	3e-04	SNP								NA				0								G	MET/VAL,MET/VAL	36,4370	41.6+/-74.8	1,34,2168	166	164	165		1771,1660	5.5	1	10	dbSNP_134	165	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	SLC39A12	NM_001145195.1,NM_152725.3	21,21	1,36,6466	AA,AG,GG	NA	0.0233,0.8171,0.2922	probably-damaging,probably-damaging	591/692,554/655	18292111	38,12968	2203	4300	6503	SO:0001583	missense				CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482	221074	221074		Solute carriers	20860	protein-coding gene	gene with protein product		608734	solute carrier family 39 (metal ion transporter), member 12		NA	12659941	Standard	NM_152725	NM_152725	NA	Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377371.3:c.1768G>A	10.37:g.18292111G>A	ENSP00000366588:p.Val590Met	NA	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	37		9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	24.0	4.485154	0.84854	0.008171	2.33E-4	ENSG00000148482	ENST00000377369;ENST00000377374;ENST00000377371;ENST00000539911;ENST00000425219	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.52789	0.1756	M	0.64080	1.96	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.995;1.0	T	0.62378	-0.6867	10	0.52906	T	0.07	-15.6242	19.7024	0.96060	0.0:0.0:1.0:0.0	.	590;591;554	Q504Y0-4;Q504Y0;Q504Y0-3	.;S39AC_HUMAN;.	M	591;554;590;457;511	ENSP00000366586:V591M;ENSP00000366591:V554M;ENSP00000366588:V590M;ENSP00000440445:V457M	ENSP00000366586:V591M	V	+	1	0	SLC39A12	18332117	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.972000	0.88022	2.724000	0.93272	0.655000	0.94253	GTG	SLC39A12-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000047060.1		+	ENST00000377371.3	Missense_Mutation	SNP	10 : 18292111 - 18292111 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	467	89
SLC45A2	51151	broad.mit.edu	37	5	33984521	33984521	+	Silent	SNP	C	C	G			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr5:33984521C>G	ENST00000382102.3	-	1	225	c.168G>C	c.(166-168)gtG>gtC	p.V56V	SLC45A2_ENST00000345083.5_Silent_p.V56V|SLC45A2_ENST00000296589.4_Silent_p.V56V|SLC45A2_ENST00000342059.3_Silent_p.V56V|SLC45A2_ENST00000509381.1_Silent_p.V56V	NM_001012509.2	NP_001012527	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	56					melanin biosynthetic process|response to stimulus|transmembrane transport|visual perception	integral to membrane|melanosome membrane				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(25)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						GGACTGGGGTCACATACGCTG	0.592		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA		Ovarian(31;380 859 8490 22203 49048)							NA				0													63	52	56			NA	NA	5		NA											NA				33984521		2203	4300	6503	SO:0001819	synonymous_variant			AF172849	CCDS3901.1, CCDS43308.1, CCDS75232.1	5p13.3	2013-08-06	2005-10-06	2005-10-06	ENSG00000164175	ENSG00000164175	51151	51151		Solute carriers	16472	protein-coding gene	gene with protein product		606202	membrane associated transporter	MATP	NA	11916009, 11574907	Standard	NM_016180	NM_001012509	NA	Approved	AIM-1, OCA4	uc003jid.3	Q9UMX9	OTTHUMG00000090719	ENST00000382102.3:c.168G>C	5.37:g.33984521C>G		NA	Q6P2P0|Q9BTM3	37	CCDS43308.1																																																																																			SLC45A2-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246885.2		-	ENST00000382102.3	Silent	SNP	5 : 33984521 - 33984521 G PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	72	16
SLIT1	6585	broad.mit.edu	37	10	98816094	98816094	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr10:98816094G>A	ENST00000266058.4	-	13	1530	c.1285C>T	c.(1285-1287)Cgg>Tgg	p.R429W	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Missense_Mutation_p.R429W	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	429					axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		TGGATGGCCCGCAGGGAGGTG	0.622		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													104	101	102			NA	NA	10		NA											NA				98816094		2203	4300	6503	SO:0001583	missense			AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122	6585	6585			11085	protein-coding gene	gene with protein product		603742	slit (Drosophila) homolog 1	SLIL1	NA	9693030, 9813312	Standard	NM_003061	NM_003061	NA	Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.1285C>T	10.37:g.98816094G>A	ENSP00000266058:p.Arg429Trp	NA	Q8WWZ2|Q9UIL7	37	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.056410	0.76074	.	.	ENSG00000187122	ENST00000266058;ENST00000371057;ENST00000371070;ENST00000314867	T;T;T	0.58210	1.8;1.8;0.35	4.91	1.86	0.25419	.	0.059286	0.64402	D	0.000002	T	0.65647	0.2711	L	0.54908	1.71	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.922	T	0.66791	-0.5834	10	0.87932	D	0	.	13.5661	0.61819	0.0:0.0:0.593:0.407	.	439;429	E7EWQ8;O75093	.;SLIT1_HUMAN	W	429;439;429;422	ENSP00000266058:R429W;ENSP00000360109:R429W;ENSP00000315005:R422W	ENSP00000266058:R429W	R	-	1	2	SLIT1	98806084	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	5.433000	0.66520	0.194000	0.20326	0.561000	0.74099	CGG	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049636.1		-	ENST00000266058.4	Missense_Mutation	SNP	10 : 98816094 - 98816094 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	362	6
SMAD4	4089	broad.mit.edu	37	18	48604697	48604698	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	AA	AA	-	-	AA	AA	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr18:48604697_48604698delAA	ENST00000588745.1	+	8	1231_1232	c.1231_1232delAA	c.(1231-1233)aaafs	p.K411fs	SMAD4_ENST00000342988.3_Frame_Shift_Del_p.K507fs|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Frame_Shift_Del_p.K507fs			Q13485	SMAD4_HUMAN	SMAD family member 4	507	MH2.				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.?(2)|p.K507Q(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)		GAGTTTTGTGAAAGGCTGGGGA	0.47		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				40	Whole gene deletion(36)|Substitution - Missense(2)|Unknown(2)	pancreas(26)|large_intestine(5)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001589	frameshift_variant			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.1231_1232delAA	18.37:g.48604697_48604698delAA	ENSP00000464901:p.Lys411fs	NA	A8K405	37	CCDS11950.1																																																																																			SMAD4-004	NOVEL	not_organism_supported|basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000449729.1		+	ENST00000588745.1	Frame_Shift_Del	DEL	18 : 48604697 - 48604698 - PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	235	61
SMU1	55234	broad.mit.edu	37	9	33068870	33068870	+	Silent	SNP	G	G	A	rs113018466	byFrequency	TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr9:33068870G>A	ENST00000397149.3	-	4	503	c.453C>T	c.(451-453)ggC>ggT	p.G151G	SMU1_ENST00000536631.1_5'UTR	NM_018225.2	NP_060695.2	Q2TAY7	SMU1_HUMAN	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	151						cytoplasm|nucleus				endometrium(2)|lung(4)|ovary(2)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)		CACTGACTTCGCCAGCTAAGG	0.507		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0								G		10,4396	17.9+/-39.9	0,10,2193	191	152	166		453	-0.1	1	9	dbSNP_132	166	0,8600		0,0,4300	no	coding-synonymous	SMU1	NM_018225.2		0,10,6493	AA,AG,GG	NA	0.0,0.227,0.0769		151/514	33068870	10,12996	2203	4300	6503	SO:0001819	synonymous_variant			AK001667	CCDS6534.1	9p12	2013-01-10			ENSG00000122692	ENSG00000122692	55234	55234		WD repeat domain containing	18247	protein-coding gene	gene with protein product	functional spliceosome-associated protein 57				NA	11438655, 11410362	Standard	NM_018225	NM_018225	NA	Approved	SMU-1, FLJ10805, BWD, fSAP57	uc003zsf.1	Q2TAY7	OTTHUMG00000019757	ENST00000397149.3:c.453C>T	9.37:g.33068870G>A		NA	Q9BU59|Q9HA96|Q9NVD1	37	CCDS6534.1																																																																																			SMU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052022.1		-	ENST00000397149.3	Silent	SNP	9 : 33068870 - 33068870 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	188	4
SORL1	6653	broad.mit.edu	37	11	121428026	121428026	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr11:121428026G>A	ENST00000260197.7	+	19	2704	c.2575G>A	c.(2575-2577)Gct>Act	p.A859T		NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	859					cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		TTGTCAGGTAGCTAATCCAGA	0.532		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													161	146	151			NA	NA	11		NA											NA				121428026		2203	4299	6502	SO:0001583	missense			Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642	6653	6653		Fibronectin type III domain containing	11185	protein-coding gene	gene with protein product	LDLR relative with 11 ligand-binding repeats	602005	chromosome 11 open reading frame 32, sortilin-related receptor, L(DLR class) A repeats-containing	C11orf32	NA	9157966, 8940146	Standard	NM_003105	NM_003105	NA	Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.2575G>A	11.37:g.121428026G>A	ENSP00000260197:p.Ala859Thr	NA	B2RNX7|Q92856	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.994993	0.54041	.	.	ENSG00000137642	ENST00000260197	D	0.91124	-2.79	5.31	5.31	0.75309	Six-bladed beta-propeller, TolB-like (1);	0.334487	0.31519	N	0.007520	D	0.91597	0.7345	M	0.74258	2.255	0.80722	D	1	B	0.27910	0.193	B	0.34536	0.185	D	0.89616	0.3845	10	0.41790	T	0.15	.	18.9779	0.92745	0.0:0.0:1.0:0.0	.	859	Q92673	SORL_HUMAN	T	859	ENSP00000260197:A859T	ENSP00000260197:A859T	A	+	1	0	SORL1	120933236	0.998000	0.40836	0.999000	0.59377	0.998000	0.95712	3.282000	0.51693	2.487000	0.83934	0.655000	0.94253	GCT	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387626.2		+	ENST00000260197.7	Missense_Mutation	SNP	11 : 121428026 - 121428026 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	389	94
SRCAP	10847	broad.mit.edu	37	16	30715613	30715613	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr16:30715613G>A	ENST00000262518.4	+	4	668	c.283G>A	c.(283-285)Gaa>Aaa	p.E95K	SRCAP_ENST00000395059.2_Missense_Mutation_p.E95K|SRCAP_ENST00000344771.4_Missense_Mutation_p.E95K	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	95					interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			GAGCCATGCCGAAATTGCAGA	0.522		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													99	98	99			NA	NA	16		NA											NA				30715613		1907	4121	6028	SO:0001583	missense			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603	10847	10847			16974	protein-coding gene	gene with protein product	Swi2/Snf2-related ATPase homolog (S. cerevisiae), domino homolog 1 (Drosophila)	611421			NA	10347196, 9205841	Standard	NM_006662	NM_006662	NA	Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.283G>A	16.37:g.30715613G>A	ENSP00000262518:p.Glu95Lys	NA	B0JZA6|O15026|Q7Z744|Q9Y5L9	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	16.05	3.011580	0.54468	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	T;T;T	0.77620	-1.11;-1.11;-1.11	4.95	4.95	0.65309	.	0.000000	0.51477	D	0.000096	T	0.70090	0.3184	N	0.08118	0	0.44985	D	0.998003	D	0.65815	0.995	P	0.52309	0.695	T	0.73777	-0.3876	10	0.38643	T	0.18	-4.5732	17.1213	0.86702	0.0:0.0:1.0:0.0	.	95	Q6ZRS2	SRCAP_HUMAN	K	95	ENSP00000262518:E95K;ENSP00000378499:E95K;ENSP00000343042:E95K	ENSP00000262518:E95K	E	+	1	0	SRCAP	30623114	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	5.090000	0.64498	2.582000	0.87167	0.650000	0.86243	GAA	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255523.1		+	ENST00000262518.4	Missense_Mutation	SNP	16 : 30715613 - 30715613 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	494	5
TBC1D1	23216	broad.mit.edu	37	4	38022213	38022213	+	Splice_Site	SNP	G	G	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr4:38022213G>A	ENST00000261439.4	+	5	1329	c.974G>A	c.(973-975)gGc>gAc	p.G325D	TBC1D1_ENST00000508802.1_Splice_Site_p.G325D	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	325	PID.					nucleus	Rab GTPase activator activity			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						CTTTGGCAGGGCATCAGACAC	0.458		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													270	259	263			NA	NA	4		NA											NA				38022213		2203	4300	6503	SO:0001630	splice_region_variant			AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882	23216	23216			11578	protein-coding gene	gene with protein product		609850			NA	10965142, 18258599	Standard	NM_015173	NM_015173	NA	Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.973-1G>A	4.37:g.38022213G>A		NA	Q96K82|Q9UPP4	37	CCDS33972.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.905016	0.92035	.	.	ENSG00000065882	ENST00000508802;ENST00000261439;ENST00000446803	T;T;T	0.14266	2.52;2.52;2.52	5.48	5.48	0.80851	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.51477	D	0.000095	T	0.36054	0.0953	L	0.54908	1.71	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.03555	-1.1025	10	0.87932	D	0	-20.7573	19.3503	0.94381	0.0:0.0:1.0:0.0	.	325;325;325	B9A6J6;E9PGH8;Q86TI0	.;.;TBCD1_HUMAN	D	325;325;196	ENSP00000423651:G325D;ENSP00000261439:G325D;ENSP00000396877:G196D	ENSP00000261439:G325D	G	+	2	0	TBC1D1	37698608	1.000000	0.71417	1.000000	0.80357	0.651000	0.38670	9.730000	0.98797	2.576000	0.86940	0.467000	0.42956	GGC	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317443.2	Missense_Mutation	+	ENST00000261439.4	Splice_Site	SNP	4 : 38022213 - 38022213 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	697	6
TMEM161B	153396	broad.mit.edu	37	5	87502295	87502295	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr5:87502295C>A	ENST00000506536.1	-	6	576	c.74G>T	c.(73-75)aGt>aTt	p.S25I	TMEM161B_ENST00000509387.1_Missense_Mutation_p.S80I|TMEM161B_ENST00000296595.6_Missense_Mutation_p.S207I|TMEM161B_ENST00000514135.1_Missense_Mutation_p.S207I|TMEM161B_ENST00000512429.1_Missense_Mutation_p.S196I|TMEM161B_ENST00000511218.1_Missense_Mutation_p.S25I			Q8NDZ6	T161B_HUMAN	transmembrane protein 161B	207						integral to membrane				endometrium(4)|large_intestine(3)|lung(9)|skin(3)|upper_aerodigestive_tract(1)	20		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)		CTGCATCGCACTGTCTGAAAA	0.279		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	5		NA											NA				87502295		2174	4261	6435	SO:0001583	missense			BC037287	CCDS4065.1, CCDS75269.1, CCDS75270.1	5q14.3	2008-02-05			ENSG00000164180	ENSG00000164180	153396	153396			28483	protein-coding gene	gene with protein product					NA	12477932	Standard	NM_153354	NM_001289008	NA	Approved	MGC33214	uc003kjc.3	Q8NDZ6	OTTHUMG00000131323	ENST00000506536.1:c.74G>T	5.37:g.87502295C>A	ENSP00000421733:p.Ser25Ile	NA	Q5CZH7|Q6UWQ6	37		.	.	.	.	.	.	.	.	.	.	C	15.63	2.891151	0.52014	.	.	ENSG00000164180	ENST00000514135;ENST00000296595;ENST00000506536;ENST00000511218;ENST00000512429;ENST00000443393;ENST00000509387	.	.	.	5.51	3.71	0.42584	.	0.186558	0.64402	D	0.000002	T	0.67382	0.2887	M	0.67397	2.05	0.80722	D	1	B;B	0.33044	0.083;0.395	P;B	0.44860	0.462;0.164	T	0.70550	-0.4841	9	0.72032	D	0.01	-7.8376	10.9255	0.47189	0.0:0.7979:0.1312:0.0709	.	25;207	B7Z6A5;Q8NDZ6	.;T161B_HUMAN	I	207;207;25;25;196;207;80	.	ENSP00000296595:S207I	S	-	2	0	TMEM161B	87538051	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.025000	0.57225	1.304000	0.44892	0.467000	0.42956	AGT	TMEM161B-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000369941.1		-	ENST00000506536.1	Missense_Mutation	SNP	5 : 87502295 - 87502295 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	71	8
TP53	7157	broad.mit.edu	37	17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	rs28934574		TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr17:7577094G>A	ENST00000420246.2	-	8	976	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000269305.4_Missense_Mutation_p.R282W	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN	tumor protein p53	282	Interaction with AXIN1 (By similarity).|Interaction with E4F1.|Interaction with HIPK1 (By similarity).		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934574).		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.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(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)		TCTGTGCGCCGGTCTCTCCCA	0.557		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	463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	large_intestine(136)|oesophagus(49)|upper_aerodigestive_tract(43)|stomach(33)|central_nervous_system(29)|breast(29)|lung(26)|ovary(21)|skin(20)|urinary_tract(16)|haematopoietic_and_lymphoid_tissue(16)|pancreas(10)|biliary_tract(5)|liver(5)|bone(5)|vulva(4)|prostate(4)|endometrium(3)|peritoneum(2)|thyroid(2)|NS(2)|autonomic_ganglia(1)|soft_tissue(1)|salivary_gland(1)	GRCh37	CM056413|CM920678	TP53	M	rs28934574	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83	71	75	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	844,844,844,844,448,448,448	1.5	0.3	17	dbSNP_125	75	2,8598	2.2+/-6.3	1,0,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	101,101,101,101,101,101,101	1,0,6502	AA,AG,GG	NA	0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	282/394,282/394,282/347,282/342,150/262,150/210,150/215	7577094	2,13004	2203	4300	6503	SO:0001583	missense	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.844C>T	17.37:g.7577094G>A	ENSP00000391127:p.Arg282Trp	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	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG	TP53-005	KNOWN	NMD_exception|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367401.1		-	ENST00000420246.2	Missense_Mutation	SNP	17 : 7577094 - 7577094 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	136	47
TRIM10	10107	broad.mit.edu	37	6	30126398	30126398	+	Silent	SNP	C	C	G			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr6:30126398C>G	ENST00000449742.2	-	3	609	c.534G>C	c.(532-534)gtG>gtC	p.V178V	TRIM10_ENST00000376704.3_Silent_p.V178V	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	178						cytoplasm	zinc ion binding			ovary(1)	1						TCTTGGTGGACACCTGAGTCT	0.537		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													162	174	170			NA	NA	6		NA											NA				30126398		1511	2709	4220	SO:0001819	synonymous_variant			Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613	10107	10107		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	10072	protein-coding gene	gene with protein product		605701	tripartite motif-containing 10	RNF9	NA	9271628, 10207104	Standard		NM_052828	NA	Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.534G>C	6.37:g.30126398C>G		NA	Q86Z08|Q96QB6|Q9C023|Q9C024	37	CCDS34375.1																																																																																			TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076634.1		-	ENST00000449742.2	Silent	SNP	6 : 30126398 - 30126398 G PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	344	5
TSC2	7249	broad.mit.edu	37	16	2136297	2136297	+	Missense_Mutation	SNP	C	C	T	rs137854039		TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr16:2136297C>T	ENST00000219476.3	+	37	5396	c.4766C>T	c.(4765-4767)cCg>cTg	p.P1589L	TSC2_ENST00000382538.6_Missense_Mutation_p.P1474L|TSC2_ENST00000350773.4_Missense_Mutation_p.P1566L|TSC2_ENST00000568454.1_Missense_Mutation_p.P1533L|TSC2_ENST00000439673.2_Missense_Mutation_p.P1486L|TSC2_ENST00000401874.2_Missense_Mutation_p.P1522L|TSC2_ENST00000353929.4_Missense_Mutation_p.P1546L	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1589	Rap-GAP.				cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				GACTGCCAGCCGGACAAGGTG	0.617		NA	D, Mis, N, F, S			hamartoma, renal cell			Tuberous Sclerosis					NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA			yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		E, O	0								C	LEU/PRO,LEU/PRO,LEU/PRO	0,4396		0,0,2198	116	92	100		4766,4565,4697	4.5	1	16		100	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	TSC2	NM_000548.3,NM_001077183.1,NM_001114382.1	98,98,98	0,1,6497	TT,TC,CC	NA	0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	1589/1808,1522/1741,1566/1785	2136297	1,12995	2198	4300	6498	SO:0001583	missense	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197	7249	7249			12363	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 160	191092		TSC4	NA	1303246, 7558029	Standard	NM_000548	NM_001077183	NA	Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.4766C>T	16.37:g.2136297C>T	ENSP00000219476:p.Pro1589Leu	NA	A7E2E2|B4DIQ7|B4DRN2|C9J378|O75275|Q4LE71|Q8TAZ1	37	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.683119	0.88542	0.0	1.16E-4	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29;-3.29	4.47	4.47	0.54385	Rap/ran-GAP (2);	0.062472	0.64402	D	0.000004	D	0.95114	0.8417	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.995;1.0;1.0;1.0	D;D;D;P;D;D;D	0.91635	0.999;0.998;0.999;0.842;0.999;0.999;0.999	D	0.92958	0.6386	10	0.15499	T	0.54	-22.8344	17.3319	0.87267	0.0:1.0:0.0:0.0	.	1474;1486;1566;364;1545;1522;1589	B4DIL8;P49815-6;P49815-4;B3KSR9;P49815-3;P49815-5;P49815	.;.;.;.;.;.;TSC2_HUMAN	L	1589;1523;1546;1486;1474;1566	ENSP00000219476:P1589L;ENSP00000248099:P1546L;ENSP00000399232:P1486L;ENSP00000371978:P1474L;ENSP00000344383:P1566L	ENSP00000219476:P1589L	P	+	2	0	TSC2	2076298	1.000000	0.71417	0.952000	0.39060	0.768000	0.43524	7.588000	0.82629	2.319000	0.78375	0.561000	0.74099	CCG	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250657.2		+	ENST00000219476.3	Missense_Mutation	SNP	16 : 2136297 - 2136297 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	187	69
TTN	7273	broad.mit.edu	37	2	179453342	179453342	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr2:179453342C>A	ENST00000589042.1	-	304	63334	c.63110G>T	c.(63109-63111)cGt>cTt	p.R21037L	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R18469L|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R11972L|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R12097L|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R12164L|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000591111.1_Missense_Mutation_p.R19396L	NM_001267550.1	NP_001254479.1	Q8WZ42	TITIN_HUMAN	titin	19396	Fibronectin type-III 52.						ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCCTTGACACGGAACTGATA	0.458		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													222	209	213			NA	NA	2		NA											NA				179453342		1913	4127	6040	SO:0001583	missense			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657	7273	7273		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	12403	protein-coding gene	gene with protein product		188840	cardiomyopathy, dilated 1G (autosomal dominant)	CMD1G	NA	2129545, 10051295	Standard	NM_133378	NM_003319	NA	Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000589042.1:c.63110G>T	2.37:g.179453342C>A	ENSP00000467141:p.Arg21037Leu	NA	E7ET18	37	CCDS59435.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.074053	0.55646	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.60920	0.15;0.15;0.15;0.15	6.16	6.16	0.99307	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.84261	0.5433	H	0.94771	3.58	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	D	0.87010	0.2122	9	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	11972;12097;12164;19396	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	18469;11972;12164;12097;11970	ENSP00000343764:R18469L;ENSP00000434586:R11972L;ENSP00000340554:R12164L;ENSP00000352154:R12097L	ENSP00000340554:R12164L	R	-	2	0	TTN	179161588	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.770000	0.85390	2.937000	0.99478	0.650000	0.86243	CGT	TTN-018	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450680.2		-	ENST00000589042.1	Missense_Mutation	SNP	2 : 179453342 - 179453342 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	537	5
VAMP4	8674	broad.mit.edu	37	1	171679889	171679889	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr1:171679889C>G	ENST00000236192.7	-	5	616	c.230G>C	c.(229-231)aGa>aCa	p.R77T	VAMP4_ENST00000482519.1_Intron|VAMP4_ENST00000415773.1_Missense_Mutation_p.R76T|VAMP4_ENST00000367740.2_Missense_Mutation_p.R76T	NM_001185127.1|NM_003762.4	NP_001172056.1|NP_003753.2	O75379	VAMP4_HUMAN	vesicle-associated membrane protein 4	77	v-SNARE coiled-coil homology.				vesicle-mediated transport	endosome|Golgi membrane|integral to membrane|lysosome				large_intestine(4)	4	all_cancers(6;1.42e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					TCTCTCCCCTCTCTCAATTAC	0.323		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													235	226	229			NA	NA	1		NA											NA				171679889		2203	4299	6502	SO:0001583	missense			AF044310	CCDS1298.1, CCDS53430.1	1q24-q25	2013-02-13			ENSG00000117533	ENSG00000117533	8674	8674		Vesicle-associated membrane proteins	12645	protein-coding gene	gene with protein product		606909			NA	9553086	Standard	NM_003762	NM_003762	NA	Approved		uc001ghx.2	O75379	OTTHUMG00000034788	ENST00000236192.7:c.230G>C	1.37:g.171679889C>G	ENSP00000236192:p.Arg77Thr	NA	A2IDD8|Q96IY9|Q96J20|Q9UEL7	37	CCDS1298.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.302646	0.81136	.	.	ENSG00000117533	ENST00000236192;ENST00000415773;ENST00000367740	T;T;T	0.53423	0.62;0.62;0.62	6.17	5.27	0.74061	Synaptobrevin (4);	0.040870	0.85682	D	0.000000	T	0.72732	0.3497	H	0.95151	3.63	0.80722	D	1	D;D	0.76494	0.994;0.999	D;D	0.72982	0.925;0.979	T	0.82946	-0.0205	10	0.87932	D	0	.	15.2816	0.73790	0.0:0.9327:0.0:0.0673	.	76;77	O75379-2;O75379	.;VAMP4_HUMAN	T	77;76;76	ENSP00000236192:R77T;ENSP00000415627:R76T;ENSP00000356714:R76T	ENSP00000236192:R77T	R	-	2	0	VAMP4	169946512	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.420000	0.73349	1.632000	0.50472	-0.140000	0.14226	AGA	VAMP4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000304033.2		-	ENST00000236192.7	Missense_Mutation	SNP	1 : 171679889 - 171679889 G PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	318	5
ZCCHC7	84186	broad.mit.edu	37	9	37349387	37349387	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr9:37349387C>T	ENST00000336755.5	+	7	1127	c.1021C>T	c.(1021-1023)Cct>Tct	p.P341S	ZCCHC7_ENST00000461038.1_3'UTR|ZCCHC7_ENST00000534928.1_Missense_Mutation_p.P51S	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	341							nucleic acid binding|zinc ion binding			central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	30				GBM - Glioblastoma multiforme(29;0.0137)		GCCGAAGACCCCTTCAAGACC	0.418		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													159	136	144			NA	NA	9		NA											NA				37349387		2203	4300	6503	SO:0001583	missense			AK026264	CCDS6608.2	9p13.1	2008-05-02			ENSG00000147905	ENSG00000147905	84186	84186		Zinc fingers, CCHC domain containing	26209	protein-coding gene	gene with protein product					NA		Standard	NM_032226	NM_032226	NA	Approved	FLJ22611, AIR1	uc003zzq.3	Q8N3Z6	OTTHUMG00000019915	ENST00000336755.5:c.1021C>T	9.37:g.37349387C>T	ENSP00000337839:p.Pro341Ser	NA	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	37	CCDS6608.2	.	.	.	.	.	.	.	.	.	.	C	9.590	1.125878	0.20959	.	.	ENSG00000147905	ENST00000336755;ENST00000534928	T;T	0.75938	-0.98;-0.98	5.7	3.63	0.41609	Zinc finger, CCHC retroviral-type (1);	0.593530	0.19292	N	0.117876	T	0.57344	0.2047	L	0.40543	1.245	0.32348	N	0.558818	B	0.20052	0.041	B	0.20767	0.031	T	0.51865	-0.8651	10	0.07813	T	0.8	-13.1561	4.7253	0.12938	0.188:0.6049:0.0:0.2071	.	341	Q8N3Z6	ZCHC7_HUMAN	S	341;51	ENSP00000337839:P341S;ENSP00000443113:P51S	ENSP00000337839:P341S	P	+	1	0	ZCCHC7	37339387	0.952000	0.32445	1.000000	0.80357	0.896000	0.52359	1.796000	0.38794	1.413000	0.46997	-0.289000	0.09944	CCT	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052453.2		+	ENST00000336755.5	Missense_Mutation	SNP	9 : 37349387 - 37349387 T PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	307	68
ZNF585A	199704	broad.mit.edu	37	19	37643142	37643142	+	Silent	SNP	G	G	A	rs113590010	byFrequency	TCGA-IB-A5SS-01A-11D-A32N-08	TCGA-IB-A5SS-10A-01D-A32N-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	4edf9fdf-c3aa-45be-a8eb-593e5e51c1bf	735bd846-c248-4ee8-a1bb-08a3f8738776	g.chr19:37643142G>A	ENST00000356958.4	-	5	1917	c.1659C>T	c.(1657-1659)caC>caT	p.H553H	ZNF585A_ENST00000355533.2_Intron|ZNF585A_ENST00000392157.2_Silent_p.H498H|ZNF585A_ENST00000292841.5_Silent_p.H498H|ZNF585A_ENST00000588723.1_Intron			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	553					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCCCACATTCGTGGCATTCAT	0.403		NA											G	2	9e-04	NA	0.01	2184	NA	0.9992	,	,	NA	4e-04	NA	NA	NA	0.0013	0.7096	LOWCOV,EXOME	NA	NA	0.0024	SNP								NA				0								G	,	6,4400	11.4+/-27.6	0,6,2197	63	63	63		1494,1494	-5.7	0	19	dbSNP_132	63	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous	ZNF585A	NM_152655.2,NM_199126.1	,	0,6,6495	AA,AG,GG	NA	0.0,0.1362,0.0461	,	498/715,498/715	37643142	6,12996	2203	4298	6501	SO:0001819	synonymous_variant			AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967	199704	199704		Zinc fingers, C2H2-type, -	26305	protein-coding gene	gene with protein product					NA	12477932	Standard	NM_152655	NM_199126	NA	Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.1659C>T	19.37:g.37643142G>A		NA	Q8TE95|Q96MV3	37																																																																																				ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000457980.2		-	ENST00000356958.4	Silent	SNP	19 : 37643142 - 37643142 A PAAD-TCGA-IB-A5SS-Tumor-SM-4WPAN	631	108
