#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
AHNAK2	113146	hgsc.bcm.edu;ucsc.edu	37	14	105412554	105412554	+	Silent	SNP	T	T	G	rs12436986	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr14:105412554T>G	ENST00000333244.5	-	7	9353	c.9234A>C	c.(9232-9234)ggA>ggC	p.G3078G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3078						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CTATCTGGGGTCCCTTGCGAT	0.627													.|||	2579	0.514976	0.5688	0.4683	5008	,	,		13838	0.3938		0.494	False		,,,				2504	0.6217																0								G		1294,2350		564,166,1092	67.0	77.0	74.0		9234	-1.0	0.0	14	dbSNP_120	74	2121,5993		930,261,2866	no	coding-synonymous	AHNAK2	NM_138420.2		1494,427,3958	GG,GT,TT		26.14,35.5104,29.0441		3078/5796	105412554	3415,8343	1822	4057	5879	SO:0001819	synonymous_variant	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.9234A>C	14.37:g.105412554T>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																				0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1		NM_138420	
AVIL	10677	hgsc.bcm.edu	37	12	58207097	58207097	+	Missense_Mutation	SNP	T	T	A			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr12:58207097T>A	ENST00000257861.3	-	3	681	c.251A>T	c.(250-252)gAc>gTc	p.D84V	RP11-571M6.18_ENST00000602327.1_lincRNA|AVIL_ENST00000537081.1_Missense_Mutation_p.D77V	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	84	Core. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					TCCCAGGTAGTCGTCCAGCTG	0.572																																																	0													159.0	142.0	148.0					12																	58207097		2203	4300	6503	SO:0001583	missense	10677			AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.251A>T	12.37:g.58207097T>A	ENSP00000257861:p.Asp84Val	Somatic		WXS	Illumina HiSeq	Phase_I	B2RAU7|Q2NKM9	Missense_Mutation	SNP	ENST00000257861.3	37	CCDS8959.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.692475	0.88735	.	.	ENSG00000135407	ENST00000537081;ENST00000257861;ENST00000549994	T;T;T	0.19105	2.17;2.17;2.17	4.93	4.93	0.64822	Gelsolin domain (1);	0.048065	0.85682	D	0.000000	T	0.49167	0.1541	M	0.84219	2.685	0.80722	D	1	D;D;D	0.67145	0.981;0.99;0.996	P;D;D	0.76575	0.743;0.967;0.988	T	0.55952	-0.8059	10	0.87932	D	0	-21.7151	13.9661	0.64209	0.0:0.0:0.0:1.0	.	77;84;84	O75366-2;F8VVU1;O75366	.;.;AVIL_HUMAN	V	77;84;84	ENSP00000443207:D77V;ENSP00000257861:D84V;ENSP00000449239:D84V	ENSP00000257861:D84V	D	-	2	0	AVIL	56493364	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.717000	0.84732	2.192000	0.70111	0.533000	0.62120	GAC		0.572	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1		NM_006576	
BPIFB6	128859	hgsc.bcm.edu;ucsc.edu	37	20	31627270	31627270	+	Missense_Mutation	SNP	A	A	C			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr20:31627270A>C	ENST00000349552.1	+	10	1018	c.1018A>C	c.(1018-1020)Atg>Ctg	p.M340L		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	340						extracellular region (GO:0005576)	lipid binding (GO:0008289)										CACCCTGGAGATGTTCGCAGC	0.532																																																	0													120.0	126.0	124.0					20																	31627270		2203	4300	6503	SO:0001583	missense	0			AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"""BPI fold containing"""	16504	protein-coding gene	gene with protein product		614110	"""bactericidal/permeability-increasing protein-like 3"""	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.1018A>C	20.37:g.31627270A>C	ENSP00000344929:p.Met340Leu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	.	.	.	.	.	.	.	.	.	.	A	2.775	-0.254839	0.05829	.	.	ENSG00000167104	ENST00000349552	T	0.08458	3.09	4.43	3.3	0.37823	.	0.341351	0.26658	N	0.023178	T	0.09818	0.0241	M	0.72479	2.2	0.27411	N	0.954587	B	0.12013	0.005	B	0.12156	0.007	T	0.26916	-1.0089	10	0.20046	T	0.44	.	7.7905	0.29116	0.7873:0.2127:0.0:0.0	.	340	Q8NFQ5	BPIB6_HUMAN	L	340	ENSP00000344929:M340L	ENSP00000344929:M340L	M	+	1	0	BPIFB6	31090931	1.000000	0.71417	0.996000	0.52242	0.019000	0.09904	1.204000	0.32296	0.709000	0.31976	0.454000	0.30748	ATG		0.532	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2		NM_174897	
C15orf40	123207	hgsc.bcm.edu	37	15	83677270	83677271	+	Intron	INS	-	-	A	rs373204607|rs534261421		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr15:83677270_83677271insA	ENST00000513601.2	-	3	374				C15orf40_ENST00000565712.1_Intron|RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000304177.5_Intron|C15orf40_ENST00000451195.3_Intron|C15orf40_ENST00000538348.2_Intron			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40											large_intestine(3)|lung(2)|skin(1)	6						gattttgtctcaaaaaaaaaaa	0.485																																																	0																																										SO:0001627	intron_variant	123207			BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.366+28->T	15.37:g.83677281_83677281dupA		Somatic		WXS	Illumina HiSeq	Phase_I	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Frame_Shift_Ins	INS	ENST00000513601.2	37	CCDS32312.2																																																																																				0.485	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2		NM_144597	
CCM2	83605	hgsc.bcm.edu;ucsc.edu	37	7	45067353	45067353	+	Intron	SNP	T	T	G			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr7:45067353T>G	ENST00000258781.6	+	2	179				CCM2_ENST00000544363.1_Intron|CCM2_ENST00000541586.1_Intron|CCM2_ENST00000474617.1_De_novo_Start_InFrame|CCM2_ENST00000475551.1_De_novo_Start_InFrame|CCM2_ENST00000381112.3_Missense_Mutation_p.I17S|CCM2_ENST00000461377.1_Intron	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2						blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						TCCAAAGAAATTCCTCAAACA	0.443																																																	0													79.0	83.0	82.0					7																	45067353		2203	4300	6503	SO:0001627	intron_variant	83605			BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"""malcavernin"""	607929	"""chromosome 7 open reading frame 22"""	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.31-10499T>G	7.37:g.45067353T>G		Somatic		WXS	Illumina HiSeq	Phase_I	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Missense_Mutation	SNP	ENST00000258781.6	37	CCDS5500.1	.	.	.	.	.	.	.	.	.	.	T	13.22	2.173631	0.38413	.	.	ENSG00000136280	ENST00000381112	T	0.48522	0.81	4.3	-5.65	0.02459	.	.	.	.	.	T	0.29749	0.0743	N	0.19112	0.55	0.09310	N	1	B;B;B	0.19200	0.013;0.034;0.013	B;B;B	0.19946	0.01;0.027;0.01	T	0.28459	-1.0043	9	0.59425	D	0.04	.	10.9092	0.47099	0.1302:0.6605:0.0:0.2093	.	17;17;17	B7Z5A6;B7Z8D5;E9PDJ3	.;.;.	S	17	ENSP00000370503:I17S	ENSP00000370503:I17S	I	+	2	0	CCM2	45033878	0.000000	0.05858	0.000000	0.03702	0.466000	0.32739	-0.296000	0.08287	-1.342000	0.02222	-0.263000	0.10527	ATT		0.443	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1		NM_031443	
CDK11A	728642	hgsc.bcm.edu;ucsc.edu	37	1	1647893	1647894	+	In_Frame_Ins	INS	-	-	TTTCTT	rs200224067|rs199866927|rs144636354		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr1:1647893_1647894insTTTCTT	ENST00000378633.1	-	5	428_429	c.349_350insAAGAAA	c.(349-351)aga>aAAGAAAga	p.116_117insKE	CDK11A_ENST00000356200.3_In_Frame_Ins_p.92_93insKE|CDK11A_ENST00000378638.2_In_Frame_Ins_p.92_93insKE|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000357760.2_In_Frame_Ins_p.116_117insKE|CDK11A_ENST00000358779.5_In_Frame_Ins_p.116_117insKE|CDK11A_ENST00000404249.3_In_Frame_Ins_p.126_127insKE|CDK11A_ENST00000378635.3_In_Frame_Ins_p.116_117insKE			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	116	Glu-rich.				apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						TTCGTGCTCTCTTTCTTTCACT	0.485																																					Pancreas(186;965 2119 30274 40311 50569)												0																																										SO:0001652	inframe_insertion	984			AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128		"""Cyclin-dependent kinases"""	1730	protein-coding gene	gene with protein product		116951	"""cell division cycle 2-like 2"", ""cell division cycle 2-like 2 (PITSLRE proteins)"""	CDC2L3, CDC2L2		7920654, 9750192, 19884882	Standard	NM_033529		Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000378633.1:c.344_349dupAAGAAA	1.37:g.1647894_1647899dupTTTCTT	ENSP00000367900:p.Lys115_Glu116dup	Somatic		WXS	Illumina HiSeq	Phase_I	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	In_Frame_Ins	INS	ENST00000378633.1	37																																																																																					0.485	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1		NM_024011	
CNTN6	27255	hgsc.bcm.edu;ucsc.edu	37	3	1269542	1269542	+	Missense_Mutation	SNP	T	T	C			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr3:1269542T>C	ENST00000446702.2	+	4	850	c.223T>C	c.(223-225)Tat>Cat	p.Y75H	CNTN6_ENST00000539053.1_Missense_Mutation_p.Y3H|CNTN6_ENST00000350110.2_Missense_Mutation_p.Y75H			Q9UQ52	CNTN6_HUMAN	contactin 6	75	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TACTATGAGTTATCACTACAG	0.403																																																	0													133.0	130.0	131.0					3																	1269542		2203	4300	6503	SO:0001583	missense	27255			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.223T>C	3.37:g.1269542T>C	ENSP00000407822:p.Tyr75His	Somatic		WXS	Illumina HiSeq	Phase_I	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	T	13.23	2.174338	0.38413	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.68624	-0.34;0.01;-0.34	5.47	4.28	0.50868	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.388068	0.22030	N	0.065611	T	0.62877	0.2464	N	0.20986	0.625	0.34226	D	0.675948	P;P	0.50819	0.712;0.939	P;P	0.55455	0.534;0.776	T	0.65236	-0.6217	10	0.15952	T	0.53	.	12.9826	0.58572	0.0:0.0:0.1347:0.8653	.	3;75	B4DGV0;Q9UQ52	.;CNTN6_HUMAN	H	75;3;75	ENSP00000407822:Y75H;ENSP00000442791:Y3H;ENSP00000341882:Y75H	ENSP00000341882:Y75H	Y	+	1	0	CNTN6	1244542	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	2.250000	0.43178	0.973000	0.38340	0.455000	0.32223	TAT		0.403	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2		NM_014461	
CUL3	8452	hgsc.bcm.edu	37	2	225422498	225422498	+	Missense_Mutation	SNP	T	T	A			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr2:225422498T>A	ENST00000264414.4	-	2	480	c.142A>T	c.(142-144)Aat>Tat	p.N48Y	CUL3_ENST00000432260.2_5'UTR|CUL3_ENST00000409096.1_Missense_Mutation_p.N24Y|CUL3_ENST00000344951.4_Intron|CUL3_ENST00000409777.1_Missense_Mutation_p.N24Y	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	48					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CCACTGTTATTCTTACGCTGG	0.363																																																	0													100.0	97.0	98.0					2																	225422498		2202	4297	6499	SO:0001583	missense	8452			U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.142A>T	2.37:g.225422498T>A	ENSP00000264414:p.Asn48Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	37	CCDS2462.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.9|21.9	4.217138|4.217138	0.79352|0.79352	.|.	.|.	ENSG00000036257|ENSG00000036257	ENST00000436172|ENST00000264414;ENST00000409096;ENST00000409777	.|T;T;T	.|0.34472	.|1.36;1.36;1.36	5.85|5.85	5.85|5.85	0.93711|0.93711	.|Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.68604|0.68604	0.3019|0.3019	M|M	0.91768|0.91768	3.24|3.24	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.81914	.|0.995;0.995	T|T	0.76719|0.76719	-0.2856|-0.2856	5|10	.|0.87932	.|D	.|0	.|.	16.2421|16.2421	0.82418|0.82418	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|26;48	.|Q53S54;Q13618	.|.;CUL3_HUMAN	V|Y	68|48;24;24	.|ENSP00000264414:N48Y;ENSP00000387200:N24Y;ENSP00000386525:N24Y	.|ENSP00000264414:N48Y	E|N	-|-	2|1	0|0	CUL3|CUL3	225130742|225130742	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.918000|7.918000	0.87506|0.87506	2.234000|2.234000	0.73211|0.73211	0.533000|0.533000	0.62120|0.62120	GAA|AAT		0.363	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			
EXO5	64789	hgsc.bcm.edu	37	1	40981245	40981246	+	Frame_Shift_Ins	INS	-	-	G	rs150018949	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr1:40981245_40981246insG	ENST00000372703.1	+	2	2103_2104	c.1029_1030insG	c.(1030-1032)cggfs	p.R344fs	EXO5_ENST00000296380.4_Frame_Shift_Ins_p.R344fs|RP11-656D10.5_ENST00000453437.1_RNA|EXO5_ENST00000358527.2_Frame_Shift_Ins_p.R344fs|RP11-656D10.6_ENST00000437060.1_RNA			Q9H790	EXO5_HUMAN	exonuclease 5	344					DNA catabolic process, exonucleolytic (GO:0000738)|interstrand cross-link repair (GO:0036297)	cytosol (GO:0005829)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)										CTTGGAAGTGCCGGACGTGTAC	0.54													-|-|G|insertion	42	0.00838658	0.0015	0.0144	5008	,	,		19343	0.0		0.0209	False		,,,				2504	0.0092																0										17,4249		0,17,2116						0.4	0.4		dbSNP_134	52	186,8064		3,180,3942	no	frameshift	DEM1	NM_022774.1		3,197,6058	A1A1,A1R,RR		2.2545,0.3985,1.6219				203,12313				SO:0001589	frameshift_variant	0			AK024797	CCDS453.1	1p34.2	2012-11-02	2012-10-30	2012-10-30	ENSG00000164002	ENSG00000164002			26115	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 176"", ""defects in morphology 1 homolog (S. cerevisiae)"""	C1orf176, DEM1		23095756	Standard	NM_022774		Approved	FLJ21144	uc001cfp.3	Q9H790	OTTHUMG00000007305	Exception_encountered	1.37:g.40981245_40981246insG	ENSP00000361788:p.Arg344fs	Somatic		WXS	Illumina HiSeq	Phase_I	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Frame_Shift_Ins	INS	ENST00000372703.1	37	CCDS453.1																																																																																				0.540	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1		NM_022774	
DICER1	23405	hgsc.bcm.edu	37	14	95597894	95597894	+	Missense_Mutation	SNP	A	A	T			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr14:95597894A>T	ENST00000526495.1	-	6	681	c.390T>A	c.(388-390)aaT>aaA	p.N130K	DICER1_ENST00000527414.1_Missense_Mutation_p.N130K|DICER1_ENST00000541352.1_Missense_Mutation_p.N130K|DICER1_ENST00000343455.3_Missense_Mutation_p.N130K|DICER1_ENST00000393063.1_Missense_Mutation_p.N130K			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	130	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		TCCAAGATGCATTTACTTCTA	0.368			"""Mis F, N"""		"""sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"""	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																														yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"""dicer 1, ribonuclease type III """		"""E, M, O"""	0													167.0	156.0	160.0					14																	95597894		2203	4300	6503	SO:0001583	missense	23405	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"""dicer 1, double-stranded RNA-specific endoribonuclease"""	606241	"""Dicer1, Dcr-1 homolog (Drosophila)"", ""multinodular goitre 1"""	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.390T>A	14.37:g.95597894A>T	ENSP00000437256:p.Asn130Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	SNP	ENST00000526495.1	37	CCDS9931.1	.	.	.	.	.	.	.	.	.	.	A	8.878	0.951037	0.18431	.	.	ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000541352	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	5.66	2.06	0.26882	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.449193	0.27460	N	0.019261	T	0.08492	0.0211	L	0.42686	1.345	0.24711	N	0.993204	B	0.11235	0.004	B	0.17979	0.02	T	0.43065	-0.9414	10	0.05959	T	0.93	-6.7176	4.8044	0.13312	0.669:0.0:0.2049:0.1262	.	130	Q9UPY3	DICER_HUMAN	K	130	ENSP00000343745:N130K;ENSP00000437256:N130K;ENSP00000376783:N130K;ENSP00000435681:N130K;ENSP00000444719:N130K	ENSP00000343745:N130K	N	-	3	2	DICER1	94667647	0.203000	0.23435	0.432000	0.26747	0.994000	0.84299	0.835000	0.27531	0.170000	0.19704	0.528000	0.53228	AAT		0.368	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			
ENAH	55740	hgsc.bcm.edu	37	1	225707051	225707051	+	Missense_Mutation	SNP	C	C	A	rs566336314|rs71170086|rs140432837	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr1:225707051C>A	ENST00000366844.3	-	5	1102	c.651G>T	c.(649-651)gaG>gaT	p.E217D	ENAH_ENST00000391874.2_5'UTR|ENAH_ENST00000284563.6_Missense_Mutation_p.E236D|ENAH_ENST00000366843.2_Missense_Mutation_p.E217D	NM_001008493.1|NM_018212.4	NP_001008493.1|NP_060682.2	Q8N8S7	ENAH_HUMAN	enabled homolog (Drosophila)	217					actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|intracellular transport (GO:0046907)|neural tube closure (GO:0001843)|T cell receptor signaling pathway (GO:0050852)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)|synapse (GO:0045202)	WW domain binding (GO:0050699)			NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)		gttcctgccgctccaggcgtt	0.602																																																	0													71.0	66.0	67.0					1																	225707051		2203	4300	6503	SO:0001583	missense	55740			AK001635	CCDS31040.1, CCDS31041.1	1q32.2	2013-08-06			ENSG00000154380	ENSG00000154380			18271	protein-coding gene	gene with protein product	"""mammalian enabled"""	609061				1420303	Standard	XM_005273182		Approved	FLJ10773, NDPP1, MENA	uc001hpc.1	Q8N8S7	OTTHUMG00000037742	ENST00000366844.3:c.651G>T	1.37:g.225707051C>A	ENSP00000355809:p.Glu217Asp	Somatic		WXS	Illumina HiSeq	Phase_I	D0PQI2|Q502W5|Q5T5M7|Q5VTQ9|Q5VTR0|Q9NVF3|Q9UFB8	Missense_Mutation	SNP	ENST00000366844.3	37	CCDS31041.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.658764	0.29515	.	.	ENSG00000154380	ENST00000366844;ENST00000366843;ENST00000284563;ENST00000538194	T;T;T	0.55052	0.54;0.54;0.54	.	.	.	.	.	.	.	.	T	0.38585	0.1046	L	0.39898	1.24	0.20074	N	0.999934	.	.	.	.	.	.	T	0.30966	-0.9960	5	0.13853	T	0.58	-3.0228	.	.	.	.	217;217	Q8N8S7-2;Q8N8S7	.;ENAH_HUMAN	D	217;217;236;216	ENSP00000355809:E217D;ENSP00000355808:E217D;ENSP00000284563:E236D	ENSP00000284563:E236D	E	-	3	2	ENAH	223773674	0.529000	0.26322	0.787000	0.31911	0.634000	0.38068	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GAG		0.602	ENAH-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357426.2		NM_018212	
FAM21C	253725	hgsc.bcm.edu	37	10	46254776	46254776	+	Missense_Mutation	SNP	A	A	C	rs199848673		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr10:46254776A>C	ENST00000336378.4	+	17	1680	c.1562A>C	c.(1561-1563)tAc>tCc	p.Y521S	FAM21C_ENST00000537517.1_Missense_Mutation_p.Y497S|FAM21C_ENST00000359860.4_Missense_Mutation_p.Y465S|FAM21C_ENST00000374362.2_Missense_Mutation_p.Y521S|FAM21C_ENST00000540872.1_Missense_Mutation_p.Y521S	NM_015262.2	NP_056077.2	Q9Y4E1	FA21C_HUMAN	family with sequence similarity 21, member C	521				Y -> S (in Ref. 1; BAA25518 and 2; BAG64168). {ECO:0000305}.	retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome (GO:0005768)|plasma membrane (GO:0005886)|WASH complex (GO:0071203)		p.Y520S(3)|p.Y521S(2)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						ACCTTATCTTACAGCAAAAAT	0.413																																																	5	Substitution - Missense(5)	prostate(4)|skin(1)						C	SER/TYR,SER/TYR,SER/TYR	254,3222		29,196,1513	61.0	73.0	69.0		1562,1490,1562	3.3	0.7	10	dbSNP_134	69	410,7550		58,294,3628	yes	missense,missense,missense	FAM21C	NM_001169106.1,NM_001169107.1,NM_015262.2	144,144,144	87,490,5141	CC,CA,AA		5.1508,7.3072,5.8062	benign,benign,benign	521/1280,497/1246,521/1321	46254776	664,10772	1738	3980	5718	SO:0001583	missense	253725				CCDS44374.1, CCDS44374.2, CCDS53528.1, CCDS53529.1	10q11.22	2014-05-09			ENSG00000172661	ENSG00000172661			23414	protein-coding gene	gene with protein product		613631				20498093	Standard	NM_015262		Approved	Em:AC012044.3, KIAA0592	uc001jcu.3	Q9Y4E1	OTTHUMG00000018089	ENST00000336378.4:c.1562A>C	10.37:g.46254776A>C	ENSP00000337541:p.Tyr521Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B4DZQ6|B9EK53|F5H0J6|F5H871|Q5SQU4|Q5SQU5|Q7L521|Q9UG79	Missense_Mutation	SNP	ENST00000336378.4	37		.	.	.	.	.	.	.	.	.	.	C	0.006	-2.057382	0.00390	0.073072	0.051508	ENSG00000172661	ENST00000336378;ENST00000540872;ENST00000537517;ENST00000374362;ENST00000399588;ENST00000359860;ENST00000436993	.	.	.	3.26	3.26	0.37387	.	0.662706	0.15995	N	0.234623	T	0.00496	0.0016	N	0.00099	-2.14	0.54753	P	1.4999999999987246E-5	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.001;0.0	T	0.25950	-1.0117	8	0.02654	T	1	0.2567	9.8043	0.40783	0.2076:0.7924:0.0:0.0	.	497;521;521;466	F5H871;Q9Y4E1-4;Q9Y4E1;Q9Y4E1-3	.;.;FA21C_HUMAN;.	S	521;521;497;521;521;465;433	.	ENSP00000337541:Y521S	Y	+	2	0	FAM21C	45574782	0.554000	0.26522	0.660000	0.29694	0.197000	0.23852	2.157000	0.42320	0.721000	0.32231	-0.488000	0.04728	TAC		0.413	FAM21C-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				
FANCD2	2177	hgsc.bcm.edu	37	3	10088404	10088404	+	Silent	SNP	C	C	T			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr3:10088404C>T	ENST00000419585.1	+	15	1436	c.1275C>T	c.(1273-1275)taC>taT	p.Y425Y	FANCD2_ENST00000287647.3_Silent_p.Y425Y|FANCD2_ENST00000383806.1_Silent_p.Y425Y|FANCD2_ENST00000383807.1_Silent_p.Y425Y			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	425					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CTGTTCATTACTTAGTAAGTG	0.353			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																														yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	0													39.0	36.0	37.0					3																	10088404		2203	4289	6492	SO:0001819	synonymous_variant	2177	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1275C>T	3.37:g.10088404C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	37	CCDS33696.1																																																																																				0.353	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			
ITGB5	3693	hgsc.bcm.edu;ucsc.edu	37	3	124482495	124482503	+	In_Frame_Del	DEL	TTGTTGAAC	TTGTTGAAC	-	rs144662766|rs150512726|rs149489624|rs140998759|rs547715576	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	TTGTTGAAC	TTGTTGAAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr3:124482495_124482503delTTGTTGAAC	ENST00000296181.4	-	15	2663_2671	c.2367_2375delGTTCAACAA	c.(2365-2376)aagttcaacaaa>aaa	p.789_792KFNK>K	ITGB5_ENST00000461306.1_5'Flank	NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	789				Missing (in Ref. 2; AAA52707). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		ATTGTAGGATTTGTTGAACTTGTTGAAGG	0.512														437	0.0872604	0.0053	0.0821	5008	,	,		26574	0.0486		0.1282	False		,,,				2504	0.1994																0										191,4075		46,99,1988						-3.5	1.0		dbSNP_129	167	1165,7089		151,863,3113	no	coding	ITGB5	NM_002213.3		197,962,5101	A1A1,A1R,RR		14.1144,4.4773,10.8307				1356,11164				SO:0001651	inframe_deletion	3693			J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"""Integrins"""	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.2367_2375delGTTCAACAA	3.37:g.124482495_124482503delTTGTTGAAC	ENSP00000296181:p.Lys789_Asn791del	Somatic		WXS	Illumina HiSeq	Phase_I	B0LPF8|B2RD70	In_Frame_Del	DEL	ENST00000296181.4	37	CCDS3030.1																																																																																				0.512	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3		NM_002213	
KAT2B	8850	hgsc.bcm.edu;ucsc.edu	37	3	20113852	20113853	+	Frame_Shift_Ins	INS	-	-	G			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr3:20113852_20113853insG	ENST00000263754.4	+	2	786_787	c.331_332insG	c.(331-333)tggfs	p.W111fs	KAT2B_ENST00000426228.1_3'UTR	NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	111					cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						ATGTAATGGCTGGAAAAACCCT	0.455																																																	0																																										SO:0001589	frameshift_variant	8850			U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"""Chromatin-modifying enzymes / K-acetyltransferases"""	8638	protein-coding gene	gene with protein product		602303	"""p300/CBP-associated factor"""	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.333dupG	3.37:g.20113854_20113854dupG	ENSP00000263754:p.Trp111fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6NSK1	Frame_Shift_Ins	INS	ENST00000263754.4	37	CCDS2634.1																																																																																				0.455	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1		NM_003884	
KIF4B	285643	hgsc.bcm.edu	37	5	154393562	154393562	+	Missense_Mutation	SNP	C	C	T			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr5:154393562C>T	ENST00000435029.4	+	1	303	c.143C>T	c.(142-144)tCc>tTc	p.S48F		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	48	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			ACTGATAAATCCTTCACCTAC	0.488																																																	0													114.0	111.0	112.0					5																	154393562		2203	4300	6503	SO:0001583	missense	285643			AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.143C>T	5.37:g.154393562C>T	ENSP00000387875:p.Ser48Phe	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	.	.	.	.	.	.	.	.	.	.	c	16.87	3.243030	0.58995	.	.	ENSG00000226650	ENST00000435029	T	0.76060	-0.99	1.48	0.455	0.16649	Kinesin, motor domain (4);	.	.	.	.	T	0.78266	0.4256	L	0.61218	1.895	0.40758	D	0.982979	P	0.44659	0.84	P	0.57009	0.811	T	0.76168	-0.3058	9	0.87932	D	0	.	7.1515	0.25614	0.0:0.7161:0.2838:0.0	.	48	Q2VIQ3	KIF4B_HUMAN	F	48	ENSP00000387875:S48F	ENSP00000387875:S48F	S	+	2	0	KIF4B	154373755	0.292000	0.24362	0.916000	0.36221	0.886000	0.51366	1.283000	0.33237	0.140000	0.18849	0.563000	0.77884	TCC		0.488	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			
KRT4	3851	hgsc.bcm.edu	37	12	53207606	53207606	+	Silent	SNP	G	G	A	rs79164931		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr12:53207606G>A	ENST00000551956.1	-	1	729	c.237C>T	c.(235-237)ggC>ggT	p.G79G	KRT4_ENST00000293774.4_Silent_p.G153G|KRT4_ENST00000458244.2_Silent_p.G59G			P19013	K2C4_HUMAN	keratin 4	79	Gly-rich.|Head.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CAGTGCCAAAGCCTCCAGCAC	0.597																																					Pancreas(190;284 2995 41444 45903)												0													85.0	102.0	96.0					12																	53207606		2113	4248	6361	SO:0001819	synonymous_variant	3851				CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.237C>T	12.37:g.53207606G>A		Somatic		WXS	Illumina HiSeq	Phase_I	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Silent	SNP	ENST00000551956.1	37	CCDS41787.2																																																																																				0.597	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1		NM_002272	
LMOD3	56203	hgsc.bcm.edu;ucsc.edu	37	3	69169051	69169056	+	In_Frame_Del	DEL	TCTTCT	TCTTCT	-	rs376142558	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	TCTTCT	TCTTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr3:69169051_69169056delTCTTCT	ENST00000420581.2	-	2	629_634	c.450_455delAGAAGA	c.(448-456)gaagaagat>gat	p.EE150del	LMOD3_ENST00000475434.1_In_Frame_Del_p.EE150del|LMOD3_ENST00000489031.1_In_Frame_Del_p.EE150del	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	150	Glu-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		atcatcatcatcttcttcttcttcat	0.359																																																	0																																										SO:0001651	inframe_deletion	56203			AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.450_455delAGAAGA	3.37:g.69169057_69169062delTCTTCT	ENSP00000414670:p.Glu150_Glu151del	Somatic		WXS	Illumina HiSeq	Phase_I	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	In_Frame_Del	DEL	ENST00000420581.2	37	CCDS46862.1																																																																																				0.359	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1		XM_067529	
MAGEC1	9947	hgsc.bcm.edu	37	X	140995291	140995291	+	Missense_Mutation	SNP	G	G	A			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chrX:140995291G>A	ENST00000285879.4	+	4	2387	c.2101G>A	c.(2101-2103)Gga>Aga	p.G701R	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	701										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					TCCTCTTGAGGGAGAGGACTC	0.562										HNSCC(15;0.026)																																							0													63.0	65.0	64.0					X																	140995291		2203	4300	6503	SO:0001583	missense	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.2101G>A	X.37:g.140995291G>A	ENSP00000285879:p.Gly701Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	g	6.772	0.511339	0.12944	.	.	ENSG00000155495	ENST00000285879	T	0.03772	3.81	0.96	-0.242	0.13039	.	.	.	.	.	T	0.02455	0.0075	N	0.19112	0.55	0.23144	N	0.998224	D	0.54964	0.969	B	0.37989	0.262	T	0.42699	-0.9436	9	0.59425	D	0.04	.	1.4094	0.02287	0.315:0.0:0.3349:0.3501	.	701	O60732	MAGC1_HUMAN	R	701	ENSP00000285879:G701R	ENSP00000285879:G701R	G	+	1	0	MAGEC1	140822957	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.574000	0.05868	0.187000	0.20147	0.190000	0.17370	GGA		0.562	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1		NM_005462	
MUC4	4585	hgsc.bcm.edu	37	3	195513772	195513772	+	Missense_Mutation	SNP	G	G	A			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr3:195513772G>A	ENST00000463781.3	-	2	5138	c.4679C>T	c.(4678-4680)tCa>tTa	p.S1560L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1560L|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTGGATACTGAGGAAGCGTC	0.577																																																	0													16.0	12.0	13.0					3																	195513772		686	1568	2254	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4679C>T	3.37:g.195513772G>A	ENSP00000417498:p.Ser1560Leu	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	4.658	0.122338	0.08931	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.57;1.56	.	.	.	.	.	.	.	.	T	0.15305	0.0369	N	0.19112	0.55	0.09310	N	1	B	0.22480	0.07	B	0.14023	0.01	T	0.28004	-1.0057	7	.	.	.	.	4.7275	0.12948	1.0E-4:0.0:0.6493:0.3506	.	1560	E7ESK3	.	L	1560	ENSP00000417498:S1560L;ENSP00000420243:S1560L	.	S	-	2	0	MUC4	196998167	0.000000	0.05858	0.018000	0.16275	0.018000	0.09664	0.230000	0.17852	0.064000	0.16427	0.064000	0.15345	TCA		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
Unknown	0	hgsc.bcm.edu	37	1	144618201	144618201	+	IGR	SNP	T	T	C	rs61809737		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr1:144618201T>C								RP11-640M9.2 (12310 upstream) : NBPF9 (193542 downstream)																							CTCCTCACTCTGGATGAGCCG	0.567																																																	0																																										SO:0001628	intergenic_variant	400818																															1.37:g.144618201T>C		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP		37																																																																																				0	0.567									
NOXA1	10811	hgsc.bcm.edu;ucsc.edu	37	9	140320783	140320783	+	Splice_Site	SNP	G	G	A			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr9:140320783G>A	ENST00000341349.2	+	2	440		c.e2+1		NOXA1_ENST00000392815.2_Splice_Site	NM_001256067.1|NM_006647.1	NP_001242996.1|NP_006638.1	Q86UR1	NOXA1_HUMAN	NADPH oxidase activator 1						positive regulation of catalytic activity (GO:0043085)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of respiratory burst (GO:0060263)|superoxide metabolic process (GO:0006801)	cytoplasm (GO:0005737)|NADPH oxidase complex (GO:0043020)	enzyme binding (GO:0019899)|Rac GTPase binding (GO:0048365)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			cervix(1)|large_intestine(2)|lung(2)|skin(3)|upper_aerodigestive_tract(1)	9	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000238)|Epithelial(140;0.000982)		AGCTGGCAAGGTGAGTACAGG	0.592																																																	0													136.0	112.0	120.0					9																	140320783		2203	4300	6503	SO:0001630	splice_region_variant	10811			AF039697	CCDS7042.1, CCDS59157.1	9q34.3	2013-09-20	2002-12-09	2002-12-13	ENSG00000188747	ENSG00000188747			10668	protein-coding gene	gene with protein product		611255	"""serologically defined colon cancer antigen 31"""	SDCCAG31		9610721	Standard	NM_001256067		Approved	NY-CO-31, FLJ25475	uc004cmu.3	Q86UR1	OTTHUMG00000131781	ENST00000341349.2:c.260+1G>A	9.37:g.140320783G>A		Somatic		WXS	Illumina HiSeq	Phase_I	O60533|Q29VU9|Q29VV0|Q2TAM1|Q8IUS3	Splice_Site	SNP	ENST00000341349.2	37	CCDS7042.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.708258	0.30322	.	.	ENSG00000188747	ENST00000341349;ENST00000392815	.	.	.	4.67	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.31629	N	0.64931	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.8489	0.35188	0.1061:0.0:0.8939:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NOXA1	139440604	0.998000	0.40836	0.025000	0.17156	0.613000	0.37349	2.926000	0.48892	0.969000	0.38237	0.550000	0.68814	.		0.592	NOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254713.1			Intron
OR4C4P	79550	hgsc.bcm.edu	37	11	48367136	48367136	+	IGR	SNP	C	C	T	rs78927905	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr11:48367136C>T								OR4C3 (19629 upstream) : OR4C5 (19900 downstream)																							AGCTTTGCGACGCCCTTCAGA	0.463													C|||	118	0.0235623	0.0847	0.0086	5008	,	,		19435	0.0		0.0	False		,,,				2504	0.0																0																																										SO:0001628	intergenic_variant	403257																															11.37:g.48367136C>T		Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP		37																																																																																				0	0.463									
OR5H6	79295	hgsc.bcm.edu;ucsc.edu	37	3	97983488	97983496	+	In_Frame_Del	DEL	TGTAACCAC	TGTAACCAC	-	rs145155372|rs149984587|rs369030566|rs398062605|rs74203917|rs372483864	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	TGTAACCAC	TGTAACCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr3:97983488_97983496delTGTAACCAC	ENST00000383696.2	+	1	401_409	c.360_368delTGTAACCAC	c.(358-369)cttgtaaccact>ctt	p.VTT124del	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	124						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						TTTTTTCCCTTGTAACCACTGTAACCACA	0.383														1588	0.317093	0.2141	0.3372	5008	,	,		24385	0.1319		0.5616	False		,,,				2504	0.3814																0										1036,3228		131,774,1227						2.2	0.0		dbSNP_134	100	4355,3849		1213,1929,960	no	coding	OR5H6	NM_001005479.1		1344,2703,2187	A1A1,A1R,RR		46.9161,24.2964,43.2387				5391,7077				SO:0001651	inframe_deletion	79295			BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"""GPCR / Class A : Olfactory receptors"""	14767	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily H, member 6"""				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.360_368delTGTAACCAC	3.37:g.97983497_97983505delTGTAACCAC	ENSP00000373196:p.Val124_Thr126del	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IF88	In_Frame_Del	DEL	ENST00000383696.2	37	CCDS33800.1																																																																																				0.383	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2			
PABPC3	5042	hgsc.bcm.edu	37	13	25671206	25671206	+	Silent	SNP	A	A	G	rs76614854		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr13:25671206A>G	ENST00000281589.3	+	1	907	c.870A>G	c.(868-870)agA>agG	p.R290R		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	290					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		GGATCACCAGATACCAGGTTG	0.398																																																	0													185.0	180.0	182.0					13																	25671206		2203	4300	6503	SO:0001819	synonymous_variant	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.870A>G	13.37:g.25671206A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	37	CCDS9311.1																																																																																				0.398	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2		NM_030979	
PABPC3	5042	hgsc.bcm.edu	37	13	25671742	25671742	+	Missense_Mutation	SNP	G	G	A	rs140135080	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr13:25671742G>A	ENST00000281589.3	+	1	1443	c.1406G>A	c.(1405-1407)cGa>cAa	p.R469Q		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	469					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		CAGGTTCCACGAGTCATGTCA	0.547																																																	0													104.0	96.0	98.0					13																	25671742		2203	4300	6503	SO:0001583	missense	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.1406G>A	13.37:g.25671742G>A	ENSP00000281589:p.Arg469Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	G	6.381	0.438497	0.12104	.	.	ENSG00000151846	ENST00000281589	T	0.26223	1.75	0.875	-0.195	0.13236	.	0.000000	0.40064	U	0.001189	T	0.13114	0.0318	L	0.35288	1.05	0.42075	D	0.991227	B	0.06786	0.001	B	0.06405	0.002	T	0.20638	-1.0269	10	0.10902	T	0.67	.	5.1429	0.14969	0.252:0.0:0.748:0.0	.	469	Q9H361	PABP3_HUMAN	Q	469	ENSP00000281589:R469Q	ENSP00000281589:R469Q	R	+	2	0	PABPC3	24569742	1.000000	0.71417	0.977000	0.42913	0.138000	0.21146	3.032000	0.49736	-0.094000	0.12374	0.313000	0.20887	CGA		0.547	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2		NM_030979	
PALB2	79728	hgsc.bcm.edu	37	16	23647298	23647298	+	Missense_Mutation	SNP	G	G	A			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr16:23647298G>A	ENST00000261584.4	-	4	721	c.569C>T	c.(568-570)tCa>tTa	p.S190L		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	190	DNA-binding (with the preference D loop > dsDNA > ssDNA).|Interaction with BRCA1.|Interaction with RAD51.				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		AGTTACTGGTGATCTAGCAGG	0.373			"""F, N, Mis"""			"""Wilms tumor, medulloblastoma, AML ,breast"""		Involved in tolerance or repair of DNA crosslinks																															yes	Rec		"""Fanconi anaemia N, breast cancer susceptibility """	16	16p12.1	79728	partner and localizer of BRCA2		"""L, O, E"""	0													176.0	180.0	179.0					16																	23647298		2197	4300	6497	SO:0001583	missense	79728				CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"""Fanconi anemia, complementation groups"""	26144	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group N"""	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.569C>T	16.37:g.23647298G>A	ENSP00000261584:p.Ser190Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.812853	0.32053	.	.	ENSG00000083093	ENST00000261584	T	0.15487	2.42	5.85	2.82	0.32997	.	1.216190	0.05676	N	0.589527	T	0.16514	0.0397	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.27400	-1.0075	10	0.66056	D	0.02	-0.0623	8.5962	0.33716	0.2507:0.0:0.7493:0.0	.	190	Q86YC2	PALB2_HUMAN	L	190	ENSP00000261584:S190L	ENSP00000261584:S190L	S	-	2	0	PALB2	23554799	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	0.415000	0.21181	0.950000	0.37743	0.655000	0.94253	TCA		0.373	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2		NM_024675	
PCNT	5116	hgsc.bcm.edu	37	21	47754449	47754449	+	Missense_Mutation	SNP	G	G	A	rs59183158		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr21:47754449G>A	ENST00000359568.5	+	3	513	c.406G>A	c.(406-408)Ggt>Agt	p.G136S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	136					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GTTCACAGTCGGTGACCACCC	0.552																																																	0													180.0	121.0	141.0					21																	47754449		2203	4300	6503	SO:0001583	missense	5116			AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.406G>A	21.37:g.47754449G>A	ENSP00000352572:p.Gly136Ser	Somatic		WXS	Illumina HiSeq	Phase_I	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	a	0.003	-2.400549	0.00195	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01279	5.06	0.158	-0.317	0.12736	.	.	.	.	.	T	0.00637	0.0021	N	0.01874	-0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49969	-0.8882	8	0.41790	T	0.15	.	.	.	.	rs59183158	18;136	O95613-2;O95613	.;PCNT_HUMAN	S	136	ENSP00000352572:G136S	ENSP00000338675:G136S	G	+	1	0	PCNT	46578877	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.839000	0.00738	-2.864000	0.00326	-2.902000	0.00092	GGT		0.552	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1		NM_006031	
PCNT	5116	hgsc.bcm.edu	37	21	47754563	47754563	+	Missense_Mutation	SNP	A	A	G	rs61735822	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr21:47754563A>G	ENST00000359568.5	+	3	627	c.520A>G	c.(520-522)Atc>Gtc	p.I174V	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	174					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GATGTTCACAATCAGTGACCA	0.537													g|||	126	0.0251597	0.0272	0.0418	5008	,	,		21389	0.0		0.0408	False		,,,				2504	0.0204																0								A	VAL/ILE	109,4297	816.6+/-416.3	0,109,2094	212.0	140.0	164.0		520	-0.5	0.0	21	dbSNP_129	164	479,8121	797.9+/-407.4	16,447,3837	no	missense	PCNT	NM_006031.5	29	16,556,5931	GG,GA,AA		5.5698,2.4739,4.521	benign	174/3337	47754563	588,12418	2203	4300	6503	SO:0001583	missense	5116			AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.520A>G	21.37:g.47754563A>G	ENSP00000352572:p.Ile174Val	Somatic		WXS	Illumina HiSeq	Phase_I	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	52	0.023809523809523808	10	0.02032520325203252	13	0.03591160220994475	0	0.0	29	0.03825857519788918	g	0	-2.861535	0.00064	0.024739	0.055698	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01246	5.11	0.235	-0.47	0.12131	.	.	.	.	.	T	0.00073	0.0002	N	0.03050	-0.425	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42716	-0.9435	8	0.02654	T	1	.	.	.	.	rs61735822	56;174	O95613-2;O95613	.;PCNT_HUMAN	V	174;161	ENSP00000352572:I174V	ENSP00000338675:I161V	I	+	1	0	PCNT	46578991	0.003000	0.15002	0.004000	0.12327	0.004000	0.04260	-1.655000	0.01982	-0.740000	0.04803	-0.741000	0.03529	ATC		0.537	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1		NM_006031	
PIWIL3	440822	hgsc.bcm.edu;ucsc.edu	37	22	25155858	25155869	+	In_Frame_Del	DEL	TGCTCCTCCTCT	TGCTCCTCCTCT	-	rs548233885|rs201419726|rs559892561	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	TGCTCCTCCTCT	TGCTCCTCCTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr22:25155858_25155869delTGCTCCTCCTCT	ENST00000332271.5	-	3	606_617	c.190_201delAGAGGAGGAGCA	c.(190-201)agaggaggagcadel	p.RGGA64del	PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000527701.1_5'UTR|PIWIL3_ENST00000533313.1_5'UTR	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	64					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						CTCCTCCTCCTGCTCCTCCTCTTGCTGCTCTT	0.575														5	0.000998403	0.0008	0.0014	5008	,	,		21733	0.0		0.003	False		,,,				2504	0.0																0																																										SO:0001651	inframe_deletion	440822			AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"""Argonaute/PIWI family"""	18443	protein-coding gene	gene with protein product		610314	"""piwi-like 3 (Drosophila)"""			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.190_201delAGAGGAGGAGCA	22.37:g.25155858_25155869delTGCTCCTCCTCT	ENSP00000330031:p.Arg64_Ala67del	Somatic		WXS	Illumina HiSeq	Phase_I		In_Frame_Del	DEL	ENST00000332271.5	37	CCDS33623.1																																																																																				0.575	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2		NM_001008496	
PLEKHA3	65977	hgsc.bcm.edu;ucsc.edu	37	2	179368497	179368497	+	Silent	SNP	C	C	T	rs139167699		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr2:179368497C>T	ENST00000234453.5	+	8	1188	c.786C>T	c.(784-786)caC>caT	p.H262H		NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	262						Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			GACCTGTTCACTGTTCAAAAA	0.358																																																	0								C		0,4406		0,0,2203	84.0	85.0	85.0		786	6.0	1.0	2	dbSNP_134	85	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PLEKHA3	NM_019091.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		262/301	179368497	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	65977			AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"""Pleckstrin homology (PH) domain containing"""	14338	protein-coding gene	gene with protein product	"""four-phosphate-adaptor protein 1"""	607774	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"""			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.786C>T	2.37:g.179368497C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q4ZG69|Q86TQ1|Q9NXT3	Silent	SNP	ENST00000234453.5	37	CCDS33336.1																																																																																				0.358	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2		NM_019091	
PRSS16	10279	hgsc.bcm.edu;ucsc.edu	37	6	27223065	27223079	+	In_Frame_Del	DEL	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	-	rs199705677|rs201493618|rs144604424|rs140280737|rs371606222|rs147170589|rs143492910|rs200987021|rs141138864|rs142712601	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr6:27223065_27223079delAAGGAGAGCCAGATT	ENST00000230582.3	+	12	1531_1545	c.1516_1530delAAGGAGAGCCAGATT	c.(1516-1530)aaggagagccagattdel	p.KESQI506del	PRSS16_ENST00000377456.2_3'UTR|PRSS16_ENST00000421826.2_In_Frame_Del_p.KESQI249del	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	506					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)	p.K506_I510delKESQI(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						CAAGCTGGCAAAGGAGAGCCAGATTAAGGGTGAAG	0.479														511	0.102037	0.1135	0.1124	5008	,	,		20927	0.0139		0.174	False		,,,				2504	0.0961				NSCLC(178;1118 2105 17078 23587 44429)												1	Deletion - In frame(1)	ovary(1)								514,3748		27,460,1644						-5.7	0.0		dbSNP_113	73	1519,6735		166,1187,2774	no	coding	PRSS16	NM_005865.3		193,1647,4418	A1A1,A1R,RR		18.4032,12.0601,16.2432				2033,10483				SO:0001651	inframe_deletion	10279			AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"""Serine peptidases / Serine peptidases"""	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.1516_1530delAAGGAGAGCCAGATT	6.37:g.27223065_27223079delAAGGAGAGCCAGATT	ENSP00000230582:p.Lys506_Ile510del	Somatic		WXS	Illumina HiSeq	Phase_I	O75416	In_Frame_Del	DEL	ENST00000230582.3	37	CCDS4623.1																																																																																				0.479	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2			
RFX5	5993	hgsc.bcm.edu	37	1	151317012	151317012	+	Splice_Site	SNP	C	C	A			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr1:151317012C>A	ENST00000290524.4	-	7	532	c.354G>T	c.(352-354)cgG>cgT	p.R118R	RFX5_ENST00000452513.2_Splice_Site_p.R78S|RP11-126K1.6_ENST00000455503.1_RNA|RP11-126K1.8_ENST00000422153.1_RNA|RFX5_ENST00000452671.2_Splice_Site_p.R118R|RFX5_ENST00000368870.2_Splice_Site_p.R118R|RFX5_ENST00000478564.1_5'Flank	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	118					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CACAGTACTTCCTGAGTGAGA	0.522																																																	0													44.0	44.0	44.0					1																	151317012		2203	4300	6503	SO:0001630	splice_region_variant	5993				CCDS994.1	1q21	2014-09-17			ENSG00000143390	ENSG00000143390			9986	protein-coding gene	gene with protein product		601863				9401005	Standard	XM_005245405		Approved		uc001exw.1	P48382	OTTHUMG00000012495	ENST00000290524.4:c.354-1G>T	1.37:g.151317012C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B7Z848|D3DV19|E9PFU4|Q5VWC3	Silent	SNP	ENST00000290524.4	37	CCDS994.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.897071	0.72639	.	.	ENSG00000143390	ENST00000452513	D	0.82711	-1.64	5.92	2.9	0.33743	.	0.102221	0.64402	D	0.000005	D	0.85835	0.5789	.	.	.	0.50632	D	0.999882	D	0.76494	0.999	D	0.87578	0.998	D	0.84807	0.0788	9	0.49607	T	0.09	.	9.1239	0.36803	0.0:0.7469:0.0:0.2531	.	78	B7Z848	.	S	78	ENSP00000398388:R78S	ENSP00000398388:R78S	R	-	3	2	RFX5	149583636	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	1.315000	0.33608	0.338000	0.23692	-0.367000	0.07326	AGG		0.522	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6		NM_000449	Silent
RP1L1	94137	hgsc.bcm.edu	37	8	10467571	10467571	+	Missense_Mutation	SNP	C	C	T	rs200175359		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr8:10467571C>T	ENST00000382483.3	-	4	4260	c.4037G>A	c.(4036-4038)gGa>gAa	p.G1346E		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1362	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		Missing (in allele RP1L1-1).|Missing (in allele RP1L1-2).		cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		ctgtccttctccttctgtttc	0.478																																																	0													87.0	83.0	84.0					8																	10467571		1931	4120	6051	SO:0001583	missense	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.4037G>A	8.37:g.10467571C>T	ENSP00000371923:p.Gly1346Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.799182	0.00617	.	.	ENSG00000183638	ENST00000382483	T	0.06068	3.35	1.72	-3.41	0.04839	.	.	.	.	.	T	0.02418	0.0074	N	0.08118	0	0.09310	N	1	B	0.28324	0.207	B	0.18561	0.022	T	0.44787	-0.9305	9	0.31617	T	0.26	.	4.437	0.11555	0.0:0.4052:0.3013:0.2935	.	1346	A6NKC6	.	E	1346	ENSP00000371923:G1346E	ENSP00000371923:G1346E	G	-	2	0	RP1L1	10504981	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-0.353000	0.07691	-0.392000	0.07751	0.109000	0.15622	GGA		0.478	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			
RP1L1	94137	hgsc.bcm.edu	37	8	10467579	10467581	+	In_Frame_Del	DEL	TTC	TTC	-	rs143686100		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr8:10467579_10467581delTTC	ENST00000382483.3	-	4	4250_4252	c.4027_4029delGAA	c.(4027-4029)gaadel	p.E1343del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1359	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		Missing (in allele RP1L1-1).|Missing (in allele RP1L1-2).		cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		ctccttctgtttctttagtttcc	0.488																																																	0																																										SO:0001651	inframe_deletion	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.4027_4029delGAA	8.37:g.10467579_10467581delTTC	ENSP00000371923:p.Glu1343del	Somatic		WXS	Illumina HiSeq	Phase_I	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																				0.488	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			
RP1L1	94137	hgsc.bcm.edu;ucsc.edu	37	8	10465965	10465965	+	Silent	SNP	T	T	C	rs112534810	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr8:10465965T>C	ENST00000382483.3	-	4	5866	c.5643A>G	c.(5641-5643)ggA>ggG	p.G1881G		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1961					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GCTGGGCCTCTCCTTCTGCCT	0.612													t|||	159	0.0317492	0.0061	0.0548	5008	,	,		16264	0.001		0.0805	False		,,,				2504	0.0317																0								T		2,3880		0,2,1939	158.0	174.0	169.0		5643	-2.8	0.0	8	dbSNP_132	169	40,8250		0,40,4105	no	coding-synonymous	RP1L1	NM_178857.5		0,42,6044	CC,CT,TT		0.4825,0.0515,0.3451		1881/2401	10465965	42,12130	1941	4145	6086	SO:0001819	synonymous_variant	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5643A>G	8.37:g.10465965T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																				0.612	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			
RP1L1	94137	hgsc.bcm.edu	37	8	10467636	10467636	+	Silent	SNP	T	T	C	rs386722179|rs4840500		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr8:10467636T>C	ENST00000382483.3	-	4	4195	c.3972A>G	c.(3970-3972)gaA>gaG	p.E1324E		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1340	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		E -> G (in allele RP1L1-3; dbSNP:rs4240659).		cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		ctgttttagtttcctctaact	0.463																																																	0													134.0	131.0	132.0					8																	10467636		1937	4124	6061	SO:0001819	synonymous_variant	94137			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3972A>G	8.37:g.10467636T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																				0.463	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			
RPGR	6103	hgsc.bcm.edu;ucsc.edu	37	X	38144799	38144799	+	Intron	SNP	C	C	A			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chrX:38144799C>A	ENST00000339363.3	-	14	2688				RPGR_ENST00000378505.2_Missense_Mutation_p.L1151F|RPGR_ENST00000338898.3_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000309513.3_Intron|TM4SF2_ENST00000465127.1_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						TTTGTTACTTCAATTCCAAGT	0.363																																																	0													99.0	87.0	91.0					X																	38144799		2202	4299	6501	SO:0001627	intron_variant	6103			U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+1547G>T	X.37:g.38144799C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		.	.	.	.	.	.	.	.	.	.	c	1.195	-0.634215	0.03584	.	.	ENSG00000156313	ENST00000378505	T	0.61158	0.13	4.03	2.23	0.28157	.	.	.	.	.	T	0.67683	0.2919	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.67103	0.949	T	0.65207	-0.6224	9	0.87932	D	0	.	6.6139	0.22766	0.0:0.5738:0.0:0.4262	.	1151	E9PE28	.	F	1151	ENSP00000367766:L1151F	ENSP00000367766:L1151F	L	-	3	2	RPGR	38029743	0.999000	0.42202	0.521000	0.27850	0.097000	0.18754	0.371000	0.20450	0.186000	0.20125	-0.450000	0.05554	TTG		0.363	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding			NM_000328	
SBDS	51119	hgsc.bcm.edu;ucsc.edu	37	7	66453385	66453385	+	Silent	SNP	T	T	C			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr7:66453385T>C	ENST00000246868.2	-	5	909	c.726A>G	c.(724-726)gtA>gtG	p.V242V		NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	242					bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						CTCCTTCTTCTACATCTTTCA	0.403			Gene Conversion			"""AML, MDS"""			Shwachman-Diamond syndrome																														yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	0													169.0	152.0	158.0					7																	66453385		2203	4300	6503	SO:0001819	synonymous_variant	51119	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.726A>G	7.37:g.66453385T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K0P4|Q96FX0|Q9NV53	Silent	SNP	ENST00000246868.2	37	CCDS5537.1																																																																																				0.403	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2		NM_016038	
SBF2	81846	hgsc.bcm.edu	37	11	9875241	9875241	+	Silent	SNP	A	A	C			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr11:9875241A>C	ENST00000256190.8	-	20	2519	c.2382T>G	c.(2380-2382)gcT>gcG	p.A794A	RP11-1H15.2_ENST00000533659.1_RNA	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	794					cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		CATAGCTCTCAGCTACACTTC	0.368																																																	0													184.0	167.0	172.0					11																	9875241		2201	4294	6495	SO:0001819	synonymous_variant	81846			AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	2135	protein-coding gene	gene with protein product	"""myotubularin related 13"""	607697	"""Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)"", ""DENN/MADD domain containing 7B"""	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.2382T>G	11.37:g.9875241A>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Silent	SNP	ENST00000256190.8	37	CCDS31427.1																																																																																				0.368	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2		NM_030962	
SLC16A9	220963	hgsc.bcm.edu	37	10	61412636	61412653	+	In_Frame_Del	DEL	CCTCCCAGCAGGACGCAG	CCTCCCAGCAGGACGCAG	-	rs200128557|rs76116242|rs576698927	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	CCTCCCAGCAGGACGCAG	CCTCCCAGCAGGACGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr10:61412636_61412653delCCTCCCAGCAGGACGCAG	ENST00000395348.3	-	6	2043_2060	c.1407_1424delCTGCGTCCTGCTGGGAGG	c.(1405-1425)ttctgcgtcctgctgggaggt>ttt	p.CVLLGG470del	SLC16A9_ENST00000395347.1_In_Frame_Del_p.CVLLGG470del	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	470					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						CAGAATAAAACCTCCCAGCAGGACGCAGAAGCCACTAA	0.427																																																	0										11,4253		0,11,2121						-11.1	0.0			77	30,8224		0,30,4097	no	coding	SLC16A9	NM_194298.2		0,41,6218	A1A1,A1R,RR		0.3635,0.258,0.3275				41,12477				SO:0001651	inframe_deletion	220963			AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"""Solute carriers"""	23520	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 9"""	614242	"""chromosome 10 open reading frame 36"", ""solute carrier family 16 (monocarboxylic acid transporters), member 9"", ""solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"""	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.1407_1424delCTGCGTCCTGCTGGGAGG	10.37:g.61412636_61412653delCCTCCCAGCAGGACGCAG	ENSP00000378757:p.Cys470_Gly475del	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZMI2|Q9UFH8	In_Frame_Del	DEL	ENST00000395348.3	37	CCDS7256.1																																																																																				0.427	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2		NM_194298	
SLC25A5	292	hgsc.bcm.edu;ucsc.edu	37	X	118603864	118603864	+	Missense_Mutation	SNP	G	G	A	rs199707714		TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chrX:118603864G>A	ENST00000317881.8	+	2	468	c.352G>A	c.(352-354)Gca>Aca	p.A118T	SLC25A5_ENST00000460013.1_3'UTR|SLC25A5-AS1_ENST00000446986.1_RNA	NM_001152.4	NP_001143.2	P05141	ADT2_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	118					adenine transport (GO:0015853)|chromosome segregation (GO:0007059)|energy reserve metabolic process (GO:0006112)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|positive regulation of cell proliferation (GO:0008284)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|MMXD complex (GO:0071817)|nucleus (GO:0005634)	adenine transmembrane transporter activity (GO:0015207)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(2)	12					Clodronate(DB00720)	AGGGAATCTGGCATCGGGTGG	0.522																																																	0																																										SO:0001583	missense	292			BC068199	CCDS14578.1	Xq24	2013-08-09			ENSG00000005022	ENSG00000005022		"""Solute carriers"""	10991	protein-coding gene	gene with protein product		300150		ANT2		2168878, 2829183	Standard	NM_001152		Approved	T2, 2F1, T3	uc004erh.4	P05141	OTTHUMG00000022715	ENST00000317881.8:c.352G>A	X.37:g.118603864G>A	ENSP00000360671:p.Ala118Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCV1|O43350	Missense_Mutation	SNP	ENST00000317881.8	37	CCDS14578.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.507272	0.64410	.	.	ENSG00000005022	ENST00000317881	T	0.79033	-1.23	4.35	4.35	0.52113	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.79435	0.4445	M	0.83852	2.665	0.80722	D	1	P	0.34997	0.479	B	0.33568	0.166	D	0.83564	0.0108	10	0.87932	D	0	.	15.2759	0.73742	0.0:0.0:1.0:0.0	.	118	P05141	ADT2_HUMAN	T	118	ENSP00000360671:A118T	ENSP00000360671:A118T	A	+	1	0	SLC25A5	118487892	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.356000	0.97091	2.100000	0.63781	0.529000	0.55759	GCA		0.522	SLC25A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058952.2		NM_001152	
SYN3	8224	hgsc.bcm.edu;ucsc.edu	37	22	32934079	32934079	+	Missense_Mutation	SNP	C	C	A			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr22:32934079C>A	ENST00000358763.2	-	9	1177	c.935G>T	c.(934-936)gGg>gTg	p.G312V	SYN3_ENST00000332840.5_Missense_Mutation_p.G312V	NM_001135774.1	NP_001129246.1	O14994	SYN3_HUMAN	synapsin III	312	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						CTTCCAGTTCCCAGAGATGGA	0.517																																																	0													171.0	150.0	157.0					22																	32934079		2203	4300	6503	SO:0001583	missense	8224			AF046873	CCDS13908.1	22q12.3	2008-05-14			ENSG00000185666	ENSG00000185666			11496	protein-coding gene	gene with protein product		602705				9539796	Standard	NM_003490		Approved		uc003amx.3	O14994	OTTHUMG00000031004	ENST00000358763.2:c.935G>T	22.37:g.32934079C>A	ENSP00000351614:p.Gly312Val	Somatic		WXS	Illumina HiSeq	Phase_I	B1B1F9	Missense_Mutation	SNP	ENST00000358763.2	37	CCDS13908.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.842156	0.71488	.	.	ENSG00000185666	ENST00000358763;ENST00000332840;ENST00000390686	T;T	0.38401	1.14;1.14	5.21	5.21	0.72293	ATP-grasp fold, subdomain 2 (1);Synapsin, ATP-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.70613	0.3244	M	0.92555	3.32	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.78831	-0.2049	10	0.87932	D	0	-4.3261	19.1343	0.93420	0.0:1.0:0.0:0.0	.	311;312;312	Q17R54;B1B1F9;O14994	.;.;SYN3_HUMAN	V	312	ENSP00000351614:G312V;ENSP00000330219:G312V	ENSP00000330219:G312V	G	-	2	0	SYN3	31264079	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	7.814000	0.86154	2.563000	0.86464	0.650000	0.86243	GGG		0.517	SYN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075892.4			
TSPAN8	7103	hgsc.bcm.edu	37	12	71526584	71526584	+	Silent	SNP	G	G	A			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr12:71526584G>A	ENST00000393330.2	-	10	1017	c.465C>T	c.(463-465)gtC>gtT	p.V155V	TSPAN8_ENST00000546561.1_Silent_p.V155V|TSPAN8_ENST00000247829.3_Silent_p.V155V|TSPAN8_ENST00000552128.1_Silent_p.V72V			P19075	TSN8_HUMAN	tetraspanin 8	155					negative regulation of blood coagulation (GO:0030195)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(2)|kidney(1)|large_intestine(3)|lung(7)|skin(3)|urinary_tract(1)	19			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)			CAGCTCCATTGACCAAACCGC	0.353																																																	0													129.0	120.0	123.0					12																	71526584		2203	4300	6503	SO:0001819	synonymous_variant	7103			M35252	CCDS8999.1	12q14.1-q21.1	2013-02-14	2005-03-21	2005-03-21		ENSG00000127324		"""Tetraspanins"""	11855	protein-coding gene	gene with protein product		600769	"""transmembrane 4 superfamily member 3"""	TM4SF3		2395876	Standard	NM_004616		Approved	CO-029	uc001swj.1	P19075		ENST00000393330.2:c.465C>T	12.37:g.71526584G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2R7T7|Q9BS78	Silent	SNP	ENST00000393330.2	37	CCDS8999.1																																																																																				0.353	TSPAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404737.1		NM_004616	
UBR5	51366	hgsc.bcm.edu	37	8	103274282	103274282	+	Missense_Mutation	SNP	A	A	T			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr8:103274282A>T	ENST00000520539.1	-	55	8309	c.7703T>A	c.(7702-7704)tTt>tAt	p.F2568Y	UBR5_ENST00000521922.1_Missense_Mutation_p.F2561Y|UBR5_ENST00000518205.1_Missense_Mutation_p.F296Y|UBR5_ENST00000220959.4_Missense_Mutation_p.F2567Y	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2568	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			AAAAAAAGCAAAATCATGCCA	0.338																																					Ovarian(131;96 1741 5634 7352 27489)												0													84.0	80.0	82.0					8																	103274282		2203	4300	6503	SO:0001583	missense	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"""Ubiquitin protein ligase E3 component n-recognins"""	16806	protein-coding gene	gene with protein product		608413	"""E3 ubiquitin protein ligase, HECT domain containing, 1"""	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.7703T>A	8.37:g.103274282A>T	ENSP00000429084:p.Phe2568Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.029783	0.75504	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000518205;ENST00000521922	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.64	5.64	0.86602	HECT (4);	0.000000	0.85682	D	0.000000	T	0.48132	0.1483	L	0.36672	1.1	0.58432	D	0.999993	D;D	0.58268	0.982;0.982	P;P	0.53593	0.73;0.73	T	0.50693	-0.8798	10	0.87932	D	0	.	15.8428	0.78864	1.0:0.0:0.0:0.0	.	2561;2568	E7EMW7;O95071	.;UBR5_HUMAN	Y	2568;2567;296;2561	ENSP00000429084:F2568Y;ENSP00000220959:F2567Y;ENSP00000428693:F296Y;ENSP00000427819:F2561Y	ENSP00000220959:F2567Y	F	-	2	0	UBR5	103343458	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	8.962000	0.93254	2.150000	0.67090	0.477000	0.44152	TTT		0.338	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2		NM_015902	
DAW1	164781	hgsc.bcm.edu	37	2	228754594	228754594	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr2:228754594G>T	ENST00000309931.2	+	3	219	c.136G>T	c.(136-138)Gaa>Taa	p.E46*	SNORA25_ENST00000607153.1_RNA|DAW1_ENST00000373666.2_Nonsense_Mutation_p.E46*|DAW1_ENST00000472604.1_3'UTR|DAW1_ENST00000545118.1_Nonsense_Mutation_p.E31*	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	46						cilium (GO:0005929)											TGCGTTAGTAGAAGAAATCCA	0.373																																																	0													85.0	82.0	83.0					2																	228754594		2203	4300	6503	SO:0001587	stop_gained	164781				CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"""WD repeat domain containing"""	26383	protein-coding gene	gene with protein product	"""outer row dynein assembly 16 homolog (Chlamydomonas)"""		"""WD repeat domain 69"""	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.136G>T	2.37:g.228754594G>T	ENSP00000311899:p.Glu46*	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZRY1|Q8N776	Nonsense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	.	.	.	.	.	.	.	.	.	.	G	31	5.100154	0.94197	.	.	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000440997;ENST00000545118	.	.	.	5.45	3.63	0.41609	.	2.034920	0.01926	N	0.040843	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	10.6887	0.45858	0.0732:0.1323:0.7945:0.0	.	.	.	.	X	46;46;31;31	.	ENSP00000311899:E46X	E	+	1	0	WDR69	228462838	0.999000	0.42202	0.329000	0.25429	0.854000	0.48673	2.818000	0.48041	0.756000	0.33013	0.650000	0.86243	GAA		0.373	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1		NM_178821	
ZNF141	7700	hgsc.bcm.edu	37	4	367267	367267	+	Silent	SNP	T	T	C	rs201021508	byFrequency	TCGA-DV-5574-01A-01D-1534-10	TCGA-DV-5574-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84a62ab5-e442-4358-9d24-572cdf7eb44e	d20fbb8f-5cd8-4dba-9d7e-8840569b2809	g.chr4:367267T>C	ENST00000240499.7	+	4	1190	c.1041T>C	c.(1039-1041)gcT>gcC	p.A347A	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	347					anatomical structure morphogenesis (GO:0009653)|limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(3)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	18						GTGGCAAAGCTTTTAGACAGT	0.423													t|||	135	0.0269569	0.0219	0.0259	5008	,	,		21511	0.0169		0.0169	False		,,,				2504	0.0552																0													41.0	44.0	43.0					4																	367267		2202	4299	6501	SO:0001819	synonymous_variant	7700			L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"""Zinc fingers, C2H2-type"", ""-"""	12926	protein-coding gene	gene with protein product		194648	"""zinc finger protein 141 (clone pHZ-44)"""	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		ENST00000240499.7:c.1041T>C	4.37:g.367267T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q6DK07	Silent	SNP	ENST00000240499.7	37	CCDS33931.1																																																																																				0.423	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1		NM_003441	
