#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_EVS_AA	i_EVS_All	i_EVS_EA	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_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
AHCYL2	23382	genome.wustl.edu	37	7	129064781	129064781	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr7:129064781C>T	ENST00000325006.3	+	14	1681	c.1627C>T	c.(1627-1629)Cag>Tag	p.Q543*	AHCYL2_ENST00000531335.2_Nonsense_Mutation_p.Q462*|AHCYL2_ENST00000490911.1_Nonsense_Mutation_p.Q440*|AHCYL2_ENST00000446212.1_Nonsense_Mutation_p.Q441*|AHCYL2_ENST00000446544.2_Nonsense_Mutation_p.Q542*|AHCYL2_ENST00000474594.1_Nonsense_Mutation_p.Q440*	NM_001130720.2|NM_015328.3	NP_001124192.1|NP_056143.1	Q96HN2	SAHH3_HUMAN	adenosylhomocysteinase-like 2	543					one-carbon metabolic process (GO:0006730)		adenosylhomocysteinase activity (GO:0004013)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	22						TGCTACTACTCAGGTAAGGCT	0.502																																					Pancreas(160;1736 1964 29875 40941 45605)	dbGAP											0													145.0	131.0	136.0					7																	129064781		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AB020635	CCDS5812.1, CCDS47706.1, CCDS47707.1, CCDS47708.1, CCDS47707.2	7q32.1	2009-06-12	2009-06-12		ENSG00000158467	ENSG00000158467			22204	protein-coding gene	gene with protein product			"""S-adenosylhomocysteine hydrolase-like 2"""				Standard	NM_001130720		Approved	KIAA0828	uc011kov.2	Q96HN2	OTTHUMG00000157677	ENST00000325006.3:c.1627C>T	7.37:g.129064781C>T	ENSP00000315931:p.Gln543*	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DIZ5|D9N155|O94917	Nonsense_Mutation	SNP	pfam_Adenosylhomocysteinase,pfam_Ado_hCys_hydrolase_NAD-bd,pfam_D-isomer_2_OHA_DH_NAD-bd,tigrfam_Adenosylhomocysteinase	p.Q543*	ENST00000325006.3	37	c.1627	CCDS5812.1	7	.	.	.	.	.	.	.	.	.	.	C	38	7.132882	0.98085	.	.	ENSG00000158467	ENST00000325006;ENST00000446544;ENST00000531335;ENST00000474594;ENST00000446212;ENST00000490911	.	.	.	5.7	5.7	0.88788	.	0.050557	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-15.1634	18.3949	0.90495	0.0:1.0:0.0:0.0	.	.	.	.	X	543;542;462;440;441;440	.	ENSP00000315931:Q543X	Q	+	1	0	AHCYL2	128852017	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.772000	0.85439	2.681000	0.91329	0.650000	0.86243	CAG	AHCYL2	-	pfam_Adenosylhomocysteinase,tigrfam_Adenosylhomocysteinase	ENSG00000158467		0.502	AHCYL2-012	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	AHCYL2	HGNC	protein_coding	OTTHUMT00000354065.1	93	0.00	0	C			129064781	129064781	+1	no_errors	ENST00000325006	ensembl	human	known	69_37n	nonsense	84	18.45	19	SNP	1.000	T
BAZ1A	11177	genome.wustl.edu	37	14	35242895	35242895	+	Missense_Mutation	SNP	C	C	G			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr14:35242895C>G	ENST00000382422.2	-	19	3362	c.3035G>C	c.(3034-3036)aGt>aCt	p.S1012T	BAZ1A_ENST00000360310.1_Missense_Mutation_p.S1012T|BAZ1A_ENST00000358716.4_Missense_Mutation_p.S980T			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1012					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		ATACCGTCCACTTTCTAATGC	0.343																																						dbGAP											0													133.0	118.0	123.0					14																	35242895		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.3035G>C	14.37:g.35242895C>G	ENSP00000371859:p.Ser1012Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Missense_Mutation	SNP	pfam_WSTF_Acf1_Cbp146,pfam_Bromodomain,pfam_DDT_dom,pfam_Znf_PHD-finger,superfamily_Bromodomain,superfamily_Znf_FYVE_PHD,smart_DDT_dom_subgr,smart_Znf_PHD,smart_Bromodomain,pfscan_WSTF_Acf1_Cbp146,pfscan_Znf_PHD-finger,pfscan_DDT_dom_superfamily,pfscan_Bromodomain,prints_Bromodomain	p.S1012T	ENST00000382422.2	37	c.3035	CCDS9651.1	14	.	.	.	.	.	.	.	.	.	.	C	8.437	0.850064	0.17034	.	.	ENSG00000198604	ENST00000358716;ENST00000382422;ENST00000360310;ENST00000543083	T;T;T	0.71817	-0.6;-0.6;-0.6	5.47	-1.99	0.07457	.	0.556215	0.22296	N	0.061924	T	0.50684	0.1630	L	0.38175	1.15	0.21782	N	0.999546	B;B	0.21309	0.043;0.054	B;B	0.23852	0.049;0.021	T	0.37103	-0.9720	10	0.10636	T	0.68	.	7.3189	0.26515	0.0:0.2793:0.1241:0.5966	.	980;1012	Q9NRL2-2;Q9NRL2	.;BAZ1A_HUMAN	T	980;1012;1012;664	ENSP00000351555:S980T;ENSP00000371859:S1012T;ENSP00000353458:S1012T	ENSP00000351555:S980T	S	-	2	0	BAZ1A	34312646	0.916000	0.31088	0.982000	0.44146	0.968000	0.65278	-0.003000	0.12901	-0.269000	0.09298	-1.283000	0.01379	AGT	BAZ1A	-	NULL	ENSG00000198604		0.343	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BAZ1A	HGNC	protein_coding	OTTHUMT00000276646.1	162	0.00	0	C			35242895	35242895	-1	no_errors	ENST00000360310	ensembl	human	known	69_37n	missense	153	12.57	22	SNP	0.675	G
C2orf71	388939	genome.wustl.edu	37	2	29295823	29295823	+	Silent	SNP	G	G	A			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr2:29295823G>A	ENST00000331664.5	-	1	1304	c.1305C>T	c.(1303-1305)ctC>ctT	p.L435L		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	435					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TTGTACTGGAGAGGCATGGGC	0.572																																						dbGAP											0													91.0	96.0	94.0					2																	29295823		2005	4160	6165	-	-	-	SO:0001819	synonymous_variant	0				CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.1305C>T	2.37:g.29295823G>A		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	NULL	p.L435	ENST00000331664.5	37	c.1305	CCDS42669.1	2																																																																																			C2orf71	-	NULL	ENSG00000179270		0.572	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	C2orf71	HGNC	protein_coding	OTTHUMT00000324924.3	70	0.00	0	G	NM_001029883		29295823	29295823	-1	no_errors	ENST00000331664	ensembl	human	novel	69_37n	silent	59	21.33	16	SNP	0.000	A
CC2D2B	387707	genome.wustl.edu	37	10	97772336	97772336	+	Missense_Mutation	SNP	G	G	C			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr10:97772336G>C	ENST00000344386.3	+	4	332	c.168G>C	c.(166-168)aaG>aaC	p.K56N	ENTPD1-AS1_ENST00000452728.1_RNA|CC2D2B_ENST00000410012.2_Missense_Mutation_p.K56N|ENTPD1-AS1_ENST00000454638.1_RNA|RP11-690P14.4_ENST00000475252.2_Intron|CC2D2B_ENST00000371198.2_Intron|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1-AS1_ENST00000451364.1_RNA	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B	56										large_intestine(1)|lung(7)|ovary(1)|urinary_tract(1)	10		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		TTTTTAAAAAGAATTGTAAGG	0.318																																						dbGAP											0													101.0	95.0	97.0					10																	97772336		1812	4074	5886	-	-	-	SO:0001583	missense	0			BC075861	CCDS41555.1, CCDS53560.1	10q23.33	2008-11-06	2007-10-19	2007-10-19	ENSG00000188649	ENSG00000188649			31666	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 130"""	C10orf130			Standard	NM_001001732		Approved	bA248J23.4	uc010qop.2	Q6DHV5	OTTHUMG00000018820	ENST00000344386.3:c.168G>C	10.37:g.97772336G>C	ENSP00000343747:p.Lys56Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Missense_Mutation	SNP	NULL	p.K56N	ENST00000344386.3	37	c.168	CCDS41555.1	10	.	.	.	.	.	.	.	.	.	.	G	6.953	0.545766	0.13312	.	.	ENSG00000188649	ENST00000424464;ENST00000451649;ENST00000410012;ENST00000344386	T;D;T	0.82433	-1.45;-1.61;-0.96	5.19	-1.1	0.09872	.	.	.	.	.	T	0.68063	0.2960	L	0.39020	1.185	0.19775	N	0.999952	B;B	0.12013	0.003;0.005	B;B	0.15052	0.006;0.012	T	0.50013	-0.8877	9	0.25751	T	0.34	.	1.0502	0.01578	0.5104:0.15:0.1938:0.1458	.	56;56	E9PCC3;Q6DHV5	.;C2D2B_HUMAN	N	117;56;56;56	ENSP00000391834:K117N;ENSP00000386988:K56N;ENSP00000343747:K56N	ENSP00000343747:K56N	K	+	3	2	CC2D2B	97762326	0.246000	0.23909	0.183000	0.23137	0.869000	0.49853	1.758000	0.38410	-0.449000	0.07117	-0.282000	0.10007	AAG	CC2D2B	-	NULL	ENSG00000188649		0.318	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	CC2D2B	HGNC	protein_coding	OTTHUMT00000049573.3	81	0.00	0	G	NM_001001732		97772336	97772336	+1	no_errors	ENST00000451649	ensembl	human	known	69_37n	missense	71	13.41	11	SNP	0.447	C
CCDC74B	91409	genome.wustl.edu	37	2	130900651	130900651	+	Intron	SNP	G	G	A			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr2:130900651G>A	ENST00000310463.6	-	2	433				CCDC74B_ENST00000409943.3_Intron|CCDC74B_ENST00000392984.3_De_novo_Start_OutOfFrame|CCDC74B_ENST00000409234.3_Silent_p.H162H|CCDC74B_ENST00000409128.1_Intron	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B											endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					AGAGCAGCACGTGCTGTGCTT	0.622																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0				CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.295+190C>T	2.37:g.130900651G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6NW18	Silent	SNP	NULL	p.H162	ENST00000310463.6	37	c.486	CCDS2155.1	2																																																																																			CCDC74B	-	NULL	ENSG00000152076		0.622	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CCDC74B	HGNC	protein_coding	OTTHUMT00000254522.3	15	0.00	0	G	NM_207310		130900651	130900651	-1	no_errors	ENST00000409234	ensembl	human	putative	69_37n	silent	9	30.77	4	SNP	0.000	A
CDH1	999	genome.wustl.edu	37	16	68867222	68867223	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr16:68867222_68867223insG	ENST00000261769.5	+	16	2660_2661	c.2469_2470insG	c.(2470-2472)gccfs	p.A824fs	CDH1_ENST00000422392.2_Frame_Shift_Ins_p.A763fs|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	824	Required for binding alpha, beta and gamma catenins.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)			NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CTGACCCCACAGCCCCGCCTTA	0.495			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																													dbGAP	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	0																																										-	-	-	SO:0001589	frameshift_variant	0	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.2470dupG	16.37:g.68867223_68867223dupG	ENSP00000261769:p.Ala824fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Frame_Shift_Ins	INS	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.A823fs	ENST00000261769.5	37	c.2469_2470	CCDS10869.1	16																																																																																			CDH1	-	pfam_Cadherin_cytoplasmic-dom	ENSG00000039068		0.495	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH1	HGNC	protein_coding	OTTHUMT00000268897.2	70	0.00	0	-	NM_004360		68867222	68867223	+1	no_errors	ENST00000261769	ensembl	human	known	69_37n	frame_shift_ins	41	24.07	13	INS	0.000:1.000	G
DNAH9	1770	genome.wustl.edu	37	17	11726261	11726261	+	Missense_Mutation	SNP	G	G	C			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr17:11726261G>C	ENST00000262442.4	+	48	9224	c.9156G>C	c.(9154-9156)caG>caC	p.Q3052H	DNAH9_ENST00000454412.2_Missense_Mutation_p.Q3052H	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3052	Stalk. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GACTCTACCAGAGCTTGTTGC	0.498																																						dbGAP											0													94.0	83.0	87.0					17																	11726261		2203	4300	6503	-	-	-	SO:0001583	missense	0			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.9156G>C	17.37:g.11726261G>C	ENSP00000262442:p.Gln3052His	Somatic		WXS	Illumina GAIIx	Phase_IV	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	pfam_Dynein_heavy,pfam_Dynein_heavy_dom-1,pfam_Dynein_heavy_dom-2,pfam_ATPase_dyneun-rel_AAA,smart_AAA+_ATPase	p.Q3052H	ENST00000262442.4	37	c.9156	CCDS11160.1	17	.	.	.	.	.	.	.	.	.	.	G	16.14	3.040216	0.55003	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.48836	0.8;0.8	4.05	4.05	0.47172	Dynein heavy chain, P-loop containing D4 domain (1);	0.327366	0.30742	N	0.008966	T	0.64136	0.2571	M	0.71036	2.16	0.80722	D	1	P	0.45126	0.851	P	0.56343	0.796	T	0.69723	-0.5068	10	0.66056	D	0.02	.	16.7695	0.85533	0.0:0.0:1.0:0.0	.	3052	Q9NYC9	DYH9_HUMAN	H	3052;3052;1634	ENSP00000262442:Q3052H;ENSP00000414874:Q3052H	ENSP00000262442:Q3052H	Q	+	3	2	DNAH9	11666986	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	2.951000	0.49089	2.233000	0.73108	0.557000	0.71058	CAG	DNAH9	-	NULL	ENSG00000007174		0.498	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNAH9	HGNC	protein_coding	OTTHUMT00000252756.2	53	0.00	0	G	NM_001372		11726261	11726261	+1	no_errors	ENST00000262442	ensembl	human	known	69_37n	missense	43	20.37	11	SNP	1.000	C
FAM171B	165215	genome.wustl.edu	37	2	187608252	187608252	+	Missense_Mutation	SNP	C	C	G			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr2:187608252C>G	ENST00000304698.5	+	3	718	c.515C>G	c.(514-516)gCa>gGa	p.A172G		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	172						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						CAAAGCCAAGCAAATATATGG	0.313																																						dbGAP											0													104.0	105.0	105.0					2																	187608252		2203	4297	6500	-	-	-	SO:0001583	missense	0			AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"""KIAA1946"""	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.515C>G	2.37:g.187608252C>G	ENSP00000304108:p.Ala172Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	pfam_Uncharacterised_FAM171	p.A172G	ENST00000304698.5	37	c.515	CCDS33347.1	2	.	.	.	.	.	.	.	.	.	.	C	17.07	3.296102	0.60086	.	.	ENSG00000144369	ENST00000304698;ENST00000272804	T	0.44083	0.93	6.02	6.02	0.97574	.	0.057177	0.64402	D	0.000001	T	0.40498	0.1119	L	0.41906	1.305	0.46701	D	0.999167	P;P	0.37061	0.58;0.58	B;B	0.38683	0.279;0.279	T	0.08743	-1.0707	10	0.33141	T	0.24	-23.9101	18.7178	0.91682	0.0:1.0:0.0:0.0	.	172;173	Q6P995;A8K122	F171B_HUMAN;.	G	172	ENSP00000304108:A172G	ENSP00000272804:A172G	A	+	2	0	FAM171B	187316497	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.282000	0.65615	2.857000	0.98124	0.650000	0.86243	GCA	FAM171B	-	pfam_Uncharacterised_FAM171	ENSG00000144369		0.313	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM171B	HGNC	protein_coding	OTTHUMT00000334679.1	90	0.00	0	C	NM_177454		187608252	187608252	+1	no_errors	ENST00000304698	ensembl	human	known	69_37n	missense	70	16.67	14	SNP	1.000	G
FBN3	84467	genome.wustl.edu	37	19	8152088	8152088	+	Missense_Mutation	SNP	G	G	T	rs145531691		TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr19:8152088G>T	ENST00000600128.1	-	54	7041	c.6627C>A	c.(6625-6627)gaC>gaA	p.D2209E	FBN3_ENST00000601739.1_Missense_Mutation_p.D2209E|FBN3_ENST00000270509.2_Missense_Mutation_p.D2209E			Q75N90	FBN3_HUMAN	fibrillin 3	2209	EGF-like 36; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CTGCACACTCGTCCACATCTT	0.632																																						dbGAP											0													78.0	67.0	71.0					19																	8152088		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.6627C>A	19.37:g.8152088G>T	ENSP00000470498:p.Asp2209Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	pfam_EGF-like_Ca-bd,pfam_TB_dom,pfam_EGF-like_dom,superfamily_TB_dom,smart_EGF-like,smart_EGF-like_Ca-bd,pirsf_Fibrillin,pfscan_EG-like_dom	p.D2209E	ENST00000600128.1	37	c.6627	CCDS12196.1	19	.	.	.	.	.	.	.	.	.	.	G	13.93	2.384213	0.42308	.	.	ENSG00000142449	ENST00000270509;ENST00000341066	D	0.95307	-3.67	3.71	2.67	0.31697	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.057156	0.64402	U	0.000003	D	0.96442	0.8839	M	0.85041	2.73	0.48087	D	0.999582	D;P	0.76494	0.999;0.896	D;P	0.71870	0.975;0.542	D	0.95117	0.8243	10	0.72032	D	0.01	.	6.9171	0.24365	0.3202:0.0:0.6798:0.0	.	2209;315	Q75N90;Q6ZNB8	FBN3_HUMAN;.	E	2209;315	ENSP00000270509:D2209E	ENSP00000270509:D2209E	D	-	3	2	FBN3	8058088	0.993000	0.37304	1.000000	0.80357	0.274000	0.26718	0.250000	0.18235	0.680000	0.31366	0.407000	0.27541	GAC	FBN3	-	pfam_EGF-like_Ca-bd,smart_EGF-like_Ca-bd,pirsf_Fibrillin,pfscan_EG-like_dom	ENSG00000142449		0.632	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FBN3	HGNC	protein_coding	OTTHUMT00000461428.2	25	0.00	0	G	NM_032447		8152088	8152088	-1	no_errors	ENST00000270509	ensembl	human	known	69_37n	missense	12	20.00	3	SNP	1.000	T
HCFC2	29915	genome.wustl.edu	37	12	104458502	104458502	+	Splice_Site	SNP	G	G	A	rs111708674		TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr12:104458502G>A	ENST00000229330.4	+	1	267		c.e1+1		GLT8D2_ENST00000548660.1_5'Flank	NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						TACAACACGGGTAGGCGCGGC	0.721																																					Esophageal Squamous(184;1814 2036 4771 6974 15702)	dbGAP											0													21.0	22.0	22.0					12																	104458502		2201	4296	6497	-	-	-	SO:0001630	splice_region_variant	0			AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727			24972	protein-coding gene	gene with protein product		607926				10196288	Standard	NM_013320		Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.163+1G>A	12.37:g.104458502G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B2R8Q5|C0H5X3	Splice_Site	SNP	-	e1+1	ENST00000229330.4	37	c.163+1	CCDS9097.1	12	.	.	.	.	.	.	.	.	.	.	G	24.1	4.488086	0.84854	.	.	ENSG00000111727	ENST00000229330	.	.	.	4.0	4.0	0.46444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6303	0.85032	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HCFC2	102982632	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	8.232000	0.89796	2.209000	0.71365	0.313000	0.20887	.	HCFC2	-	-	ENSG00000111727		0.721	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HCFC2	HGNC	protein_coding	OTTHUMT00000407780.1	20	0.00	0	G	NM_013320	Intron	104458502	104458502	+1	no_errors	ENST00000229330	ensembl	human	known	69_37n	splice_site	9	30.77	4	SNP	1.000	A
LYST	1130	genome.wustl.edu	37	1	235922292	235922292	+	Missense_Mutation	SNP	G	G	T			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr1:235922292G>T	ENST00000389794.3	-	23	7035	c.6861C>A	c.(6859-6861)aaC>aaA	p.N2287K	LYST_ENST00000389793.2_Missense_Mutation_p.N2287K			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2287					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TTGCAGTTCGGTTGTAATTTG	0.423																																						dbGAP											0													77.0	70.0	72.0					1																	235922292		2203	4300	6503	-	-	-	SO:0001583	missense	0			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.6861C>A	1.37:g.235922292G>T	ENSP00000374444:p.Asn2287Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	pfam_BEACH_dom,pfam_WD40_repeat,superfamily_BEACH_dom,superfamily_WD40_repeat_dom,superfamily_ARM-type_fold,smart_WD40_repeat,pfscan_BEACH_dom,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.N2287K	ENST00000389794.3	37	c.6861	CCDS31062.1	1	.	.	.	.	.	.	.	.	.	.	G	8.408	0.843491	0.16963	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.61392	0.11;0.11	4.93	3.01	0.34805	.	1.518450	0.03156	N	0.168638	T	0.51500	0.1678	L	0.44542	1.39	0.22541	N	0.999006	B	0.02656	0.0	B	0.04013	0.001	T	0.30822	-0.9965	10	0.13108	T	0.6	.	10.9256	0.47189	0.0714:0.3276:0.6011:0.0	.	2287	Q99698	LYST_HUMAN	K	2287	ENSP00000374444:N2287K;ENSP00000374443:N2287K	ENSP00000374443:N2287K	N	-	3	2	LYST	233988915	0.007000	0.16637	0.000000	0.03702	0.908000	0.53690	1.414000	0.34736	0.589000	0.29677	0.558000	0.71614	AAC	LYST	-	superfamily_ARM-type_fold	ENSG00000143669		0.423	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LYST	HGNC	protein_coding	OTTHUMT00000097533.5	53	0.00	0	G			235922292	235922292	-1	no_errors	ENST00000389793	ensembl	human	known	69_37n	missense	31	11.43	4	SNP	0.010	T
MAP3K5	4217	genome.wustl.edu	37	6	137019707	137019707	+	Silent	SNP	G	G	A			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr6:137019707G>A	ENST00000359015.4	-	4	1086	c.726C>T	c.(724-726)ttC>ttT	p.F242F		NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	242					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		GAAGCAGCTCGAAGTTCGGTT	0.418																																						dbGAP											0													141.0	122.0	128.0					6																	137019707		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6857	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 1"""	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.726C>T	6.37:g.137019707G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_SAM/pointed,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.F242	ENST00000359015.4	37	c.726	CCDS5179.1	6																																																																																			MAP3K5	-	NULL	ENSG00000197442		0.418	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MAP3K5	HGNC	protein_coding	OTTHUMT00000042383.1	90	0.00	0	G			137019707	137019707	-1	no_errors	ENST00000359015	ensembl	human	known	69_37n	silent	49	23.44	15	SNP	0.902	A
MICALL1	85377	genome.wustl.edu	37	22	38333086	38333086	+	Splice_Site	SNP	G	G	A			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr22:38333086G>A	ENST00000215957.6	+	14	2434		c.e14-1		MICALL1_ENST00000402631.1_Splice_Site	NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1						endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					TCCCTGGGCAGAAAAGGACTG	0.612																																						dbGAP											0													56.0	61.0	60.0					22																	38333086		1902	3603	5505	-	-	-	SO:0001630	splice_region_variant	0			BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"""molecule interacting with Rab13"""					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.2309-1G>A	22.37:g.38333086G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Splice_Site	SNP	-	e14-1	ENST00000215957.6	37	c.2309-1	CCDS13961.1	22	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333502	0.81801	.	.	ENSG00000100139	ENST00000215957;ENST00000454685;ENST00000402631;ENST00000424008	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8776	0.92345	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MICALL1	36663032	1.000000	0.71417	0.962000	0.40283	0.802000	0.45316	7.674000	0.83992	2.453000	0.82957	0.596000	0.82720	.	MICALL1	-	-	ENSG00000100139		0.612	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MICALL1	HGNC	protein_coding	OTTHUMT00000319545.4	52	0.00	0	G	NM_033386	Intron	38333086	38333086	+1	no_errors	ENST00000215957	ensembl	human	known	69_37n	splice_site	41	16.33	8	SNP	1.000	A
MUS81	80198	genome.wustl.edu	37	11	65632261	65632261	+	Missense_Mutation	SNP	C	C	T			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr11:65632261C>T	ENST00000308110.4	+	12	1596	c.1247C>T	c.(1246-1248)aCg>aTg	p.T416M	EFEMP2_ENST00000532648.1_5'Flank|MUS81_ENST00000533035.1_Missense_Mutation_p.T341M	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	416					DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		GCCCTCTTGACGCGGGGCCTG	0.592								Homologous recombination																														dbGAP											0													52.0	52.0	52.0					11																	65632261		2201	4296	6497	-	-	-	SO:0001583	missense	0				CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"""SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	606591	"""MUS81 endonuclease homolog (yeast)"", ""MUS81 endonuclease homolog (S. cerevisiae)"""			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.1247C>T	11.37:g.65632261C>T	ENSP00000307853:p.Thr416Met	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9H7D9	Missense_Mutation	SNP	pfam_ERCC4_domain,superfamily_Restrct_endonuc-II-like,superfamily_DNA-dir_DNA_pol_X_beta-like_N,smart_ERCC4_domain	p.T416M	ENST00000308110.4	37	c.1247	CCDS8115.1	11	.	.	.	.	.	.	.	.	.	.	C	21.8	4.198255	0.79015	.	.	ENSG00000172732	ENST00000533035;ENST00000308110;ENST00000437855	T;T	0.32988	1.43;1.43	5.92	5.92	0.95590	DNA repair nuclease, XPF-type/Helicase (1);Restriction endonuclease, type II-like (1);	0.111718	0.64402	D	0.000004	T	0.63082	0.2481	M	0.86651	2.83	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67425	-0.5674	10	0.72032	D	0.01	-6.0655	17.8066	0.88602	0.0:1.0:0.0:0.0	.	416	Q96NY9	MUS81_HUMAN	M	341;416;416	ENSP00000432287:T341M;ENSP00000307853:T416M	ENSP00000307853:T416M	T	+	2	0	MUS81	65388837	1.000000	0.71417	0.350000	0.25708	0.784000	0.44337	6.689000	0.74562	2.808000	0.96608	0.561000	0.74099	ACG	MUS81	-	superfamily_Restrct_endonuc-II-like	ENSG00000172732		0.592	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MUS81	HGNC	protein_coding	OTTHUMT00000390941.3	57	0.00	0	C	NM_025128		65632261	65632261	+1	no_errors	ENST00000308110	ensembl	human	known	69_37n	missense	39	25.00	13	SNP	0.998	T
NMUR2	56923	genome.wustl.edu	37	5	151771792	151771792	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr5:151771792G>T	ENST00000255262.3	-	4	1373	c.1208C>A	c.(1207-1209)tCa>tAa	p.S403*		NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	403					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			GTTTGTTCTTGACATCTGTTC	0.448																																						dbGAP											0													153.0	161.0	158.0					5																	151771792		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"""GPCR / Class A : Neuromedin U receptors"""	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.1208C>A	5.37:g.151771792G>T	ENSP00000255262:p.Ser403*	Somatic		WXS	Illumina GAIIx	Phase_IV	Q7LC54|Q96AM5|Q9NRA6	Nonsense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_supfam,prints_NeuromedU_rcpt_2,prints_NeuromedU_rcpt,prints_7TM_GPCR_Rhodpsn	p.S403*	ENST00000255262.3	37	c.1208	CCDS4321.1	5	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390120	0.61956	.	.	ENSG00000132911	ENST00000255262	.	.	.	3.71	-0.269	0.12930	.	33.020300	0.00166	N	0.000000	.	.	.	.	.	.	0.30135	N	0.804425	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	10.1034	0.7212	0.00941	0.1942:0.1568:0.3288:0.3202	.	.	.	.	X	403	.	ENSP00000255262:S403X	S	-	2	0	NMUR2	151751985	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.551000	0.06027	-0.068000	0.12953	0.467000	0.42956	TCA	NMUR2	-	NULL	ENSG00000132911		0.448	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NMUR2	HGNC	protein_coding	OTTHUMT00000252439.1	158	0.00	0	G	NM_020167		151771792	151771792	-1	no_errors	ENST00000255262	ensembl	human	known	69_37n	nonsense	118	18.06	26	SNP	0.000	T
NOC4L	79050	genome.wustl.edu	37	12	132631861	132631861	+	Missense_Mutation	SNP	G	G	T			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr12:132631861G>T	ENST00000330579.1	+	4	422	c.381G>T	c.(379-381)caG>caT	p.Q127H	DDX51_ENST00000397333.3_5'Flank	NM_024078.1	NP_076983.1	Q9BVI4	NOC4L_HUMAN	nucleolar complex associated 4 homolog (S. cerevisiae)	127					rRNA processing (GO:0006364)	integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|skin(2)	14	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.2e-08)|Epithelial(86;3.34e-07)|all cancers(50;1.97e-05)		AGTTCGTGCAGCTGGAAGGAG	0.647																																						dbGAP											0													34.0	33.0	33.0					12																	132631861		2182	4285	6467	-	-	-	SO:0001583	missense	0				CCDS9277.1	12q24.33	2011-08-12			ENSG00000184967	ENSG00000184967			28461	protein-coding gene	gene with protein product		612819				12446671	Standard	NM_024078		Approved	MGC3162, NET49, UTP19	uc001ujz.1	Q9BVI4	OTTHUMG00000168260	ENST00000330579.1:c.381G>T	12.37:g.132631861G>T	ENSP00000328854:p.Gln127His	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N2S5|Q96I14	Missense_Mutation	SNP	pfam_CCAAT-binding_factor,superfamily_ARM-type_fold	p.Q127H	ENST00000330579.1	37	c.381	CCDS9277.1	12	.	.	.	.	.	.	.	.	.	.	G	15.23	2.771088	0.49680	.	.	ENSG00000184967	ENST00000330579;ENST00000541954	T;T	0.64260	-0.09;1.47	4.72	4.72	0.59763	Armadillo-like helical (1);	0.337351	0.30723	N	0.009019	T	0.72020	0.3409	M	0.71581	2.175	0.80722	D	1	D	0.63880	0.993	P	0.59703	0.862	T	0.74535	-0.3633	10	0.59425	D	0.04	-40.9426	9.5354	0.39220	0.1386:0.0:0.8614:0.0	.	127	Q9BVI4	NOC4L_HUMAN	H	127;94	ENSP00000328854:Q127H;ENSP00000438255:Q94H	ENSP00000328854:Q127H	Q	+	3	2	NOC4L	131197814	0.996000	0.38824	1.000000	0.80357	0.506000	0.33950	2.257000	0.43240	2.135000	0.66039	0.478000	0.44815	CAG	NOC4L	-	superfamily_ARM-type_fold	ENSG00000184967		0.647	NOC4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NOC4L	HGNC	protein_coding	OTTHUMT00000398999.1	25	0.00	0	G	NM_024078		132631861	132631861	+1	no_errors	ENST00000330579	ensembl	human	known	69_37n	missense	14	17.65	3	SNP	0.999	T
NUDC	10726	genome.wustl.edu	37	1	27268243	27268243	+	Splice_Site	SNP	G	G	A			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr1:27268243G>A	ENST00000321265.5	+	4	486		c.e4-1			NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein						cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)				cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)		CTTTGCCCCAGAAAAAGGATG	0.587																																						dbGAP											0													61.0	57.0	58.0					1																	27268243		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0				CCDS292.1	1p35-p34	2013-08-06	2013-08-06		ENSG00000090273	ENSG00000090273			8045	protein-coding gene	gene with protein product		610325	"""nuclear distribution gene C homolog (A. nidulans)"", ""nuclear distribution C homolog (A. nidulans)"""				Standard	NM_006600		Approved	NudC	uc001bng.2	Q9Y266	OTTHUMG00000004226	ENST00000321265.5:c.364-1G>A	1.37:g.27268243G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	Splice_Site	SNP	-	e4-1	ENST00000321265.5	37	c.364-1	CCDS292.1	1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.399449	0.42512	.	.	ENSG00000090273	ENST00000435827;ENST00000321265;ENST00000452707	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8538	0.46786	0.0893:0.0:0.9106:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NUDC	27140830	1.000000	0.71417	0.997000	0.53966	0.548000	0.35241	4.071000	0.57556	2.452000	0.82932	0.655000	0.94253	.	NUDC	-	-	ENSG00000090273		0.587	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NUDC	HGNC	protein_coding	OTTHUMT00000012172.2	40	0.00	0	G		Intron	27268243	27268243	+1	no_errors	ENST00000321265	ensembl	human	known	69_37n	splice_site	46	16.36	9	SNP	0.994	A
PCDHA3	56145	genome.wustl.edu	37	5	140180891	140180891	+	Missense_Mutation	SNP	G	G	A			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr5:140180891G>A	ENST00000522353.2	+	1	109	c.109G>A	c.(109-111)Gag>Aag	p.E37K	PCDHA3_ENST00000532566.2_Missense_Mutation_p.E37K|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	37	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCGTCTCTGAGGAGGCCAA	0.672																																						dbGAP											0													58.0	64.0	62.0					5																	140180891		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.109G>A	5.37:g.140180891G>A	ENSP00000429808:p.Glu37Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	O75286	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.E37K	ENST00000522353.2	37	c.109	CCDS54915.1	5	.	.	.	.	.	.	.	.	.	.	g	19.89	3.911409	0.72983	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.60299	0.2;0.2	4.65	4.65	0.58169	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	0.000000	0.39341	U	0.001399	D	0.87034	0.6077	H	0.99565	4.63	0.44289	D	0.997157	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.93241	0.6626	10	0.87932	D	0	.	17.9484	0.89045	0.0:0.0:1.0:0.0	.	37;37	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	K	37	ENSP00000429808:E37K;ENSP00000434086:E37K	ENSP00000429808:E37K	E	+	1	0	PCDHA3	140161075	1.000000	0.71417	0.814000	0.32528	0.316000	0.28119	9.574000	0.98184	2.312000	0.78011	0.586000	0.80456	GAG	PCDHA3	-	pfam_Cadherin_N,superfamily_Cadherin-like,pfscan_Cadherin	ENSG00000255408		0.672	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHA3	HGNC	protein_coding	OTTHUMT00000372848.2	53	0.00	0	G	NM_018906		140180891	140180891	+1	no_errors	ENST00000522353	ensembl	human	known	69_37n	missense	62	11.43	8	SNP	0.999	A
PIK3CA	5290	genome.wustl.edu	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003		TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr3:178936091G>A	ENST00000263967.3	+	10	1790	c.1633G>A	c.(1633-1635)Gag>Aag	p.E545K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545K(881)|p.E545Q(18)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAATCACTGAGCAGGAGAA	0.353	E545K(BC3C_URINARY_TRACT)|E545K(BFTC909_KIDNEY)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(HCC202_BREAST)|E545K(HCT15_LARGE_INTESTINE)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(KYSE510_OESOPHAGUS)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(MCF7_BREAST)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(NCIH460_LUNG)|E545K(NCIH508_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(RERFLCSQ1_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	899	Substitution - Missense(899)	breast(308)|large_intestine(286)|urinary_tract(97)|lung(44)|endometrium(37)|ovary(25)|stomach(17)|upper_aerodigestive_tract(16)|skin(14)|central_nervous_system(13)|cervix(13)|thyroid(7)|oesophagus(7)|penis(4)|kidney(3)|soft_tissue(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|NS(1)|pituitary(1)											61.0	60.0	60.0					3																	178936091		1813	4072	5885	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1633G>A	3.37:g.178936091G>A	ENSP00000263967:p.Glu545Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.E545K	ENST00000263967.3	37	c.1633	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	G	36	5.703347	0.96812	.	.	ENSG00000121879	ENST00000263967	T	0.63255	-0.03	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	L	0.51914	1.62	0.80722	D	1	D	0.62365	0.991	D	0.62955	0.909	T	0.68872	-0.5294	10	0.32370	T	0.25	-25.7963	20.0024	0.97423	0.0:0.0:1.0:0.0	.	545	P42336	PK3CA_HUMAN	K	545	ENSP00000263967:E545K	ENSP00000263967:E545K	E	+	1	0	PIK3CA	180418785	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAG	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	77	0.00	0	G			178936091	178936091	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	40	27.27	15	SNP	1.000	A
PRDM15	63977	genome.wustl.edu	37	21	43223022	43223023	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr21:43223022_43223023insT	ENST00000269844.3	-	30	4000_4001	c.3890_3891insA	c.(3889-3891)aagfs	p.K1297fs	PRDM15_ENST00000422911.1_Frame_Shift_Ins_p.K988fs|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000398548.1_Frame_Shift_Ins_p.K968fs|PRDM15_ENST00000538201.1_Frame_Shift_Ins_p.K951fs|PRDM15_ENST00000447207.2_Frame_Shift_Ins_p.K931fs	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1297					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						TGTGACTTCGCTTGGCAGCTTT	0.564																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.3891dupA	21.37:g.43223024_43223024dupT	ENSP00000269844:p.Lys1297fs	Somatic		WXS	Illumina GAIIx	Phase_IV	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Frame_Shift_Ins	INS	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_SET_dom,pfscan_Znf_C2H2	p.R1298fs	ENST00000269844.3	37	c.3891_3890	CCDS13676.1	21																																																																																			PRDM15	-	NULL	ENSG00000141956		0.564	PRDM15-201	KNOWN	basic|CCDS	protein_coding	PRDM15	HGNC	protein_coding		46	0.00	0	-	NM_022115		43223022	43223023	-1	no_errors	ENST00000269844	ensembl	human	known	69_37n	frame_shift_ins	46	25.81	16	INS	0.837:0.945	T
PSMA1	5682	genome.wustl.edu	37	11	14535994	14535994	+	Missense_Mutation	SNP	C	C	T			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr11:14535994C>T	ENST00000396394.2	-	5	694	c.298G>A	c.(298-300)Gat>Aat	p.D100N	PSMA1_ENST00000555531.1_Missense_Mutation_p.D100N|PSMA1_ENST00000396393.1_Missense_Mutation_p.D100N|PSMA1_ENST00000419365.2_Missense_Mutation_p.D100N|PSMA1_ENST00000530457.1_Missense_Mutation_p.D75N|PSMA1_ENST00000418988.2_Missense_Mutation_p.D106N	NM_002786.3	NP_002777.1	P25786	PSA1_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 1	100					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysome (GO:0005844)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	RNA binding (GO:0003723)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	3						AGTGGTCTATCGAATACAAAT	0.318																																						dbGAP											0													51.0	48.0	49.0					11																	14535994		2200	4293	6493	-	-	-	SO:0001583	missense	0			X61969	CCDS7816.1, CCDS31431.1	11p15.1	2005-10-10			ENSG00000129084	ENSG00000129084		"""Proteasome (prosome, macropain) subunits"""	9530	protein-coding gene	gene with protein product		602854				1398136, 2025653	Standard	NM_148976		Approved	HC2, NU, PROS30, MGC14542, MGC14575, MGC14751, MGC1667, MGC21459, MGC22853, MGC23915	uc001mlk.3	P25786	OTTHUMG00000165825	ENST00000396394.2:c.298G>A	11.37:g.14535994C>T	ENSP00000379676:p.Asp100Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K400|Q53YE8|Q9BRV9	Missense_Mutation	SNP	pfam_Proteasome_sua/b,pfam_Proteasome_asu_N,smart_Proteasome_asu_N	p.D106N	ENST00000396394.2	37	c.316	CCDS7816.1	11	.	.	.	.	.	.	.	.	.	.	C	16.42	3.117007	0.56505	.	.	ENSG00000129084	ENST00000419365;ENST00000396394;ENST00000396393;ENST00000530457;ENST00000418988	T;T;T;T;T	0.41065	1.02;1.01;1.01;1.01;1.01	5.57	5.57	0.84162	.	0.041428	0.85682	D	0.000000	T	0.35828	0.0945	L	0.37697	1.125	0.80722	D	1	B;B;B	0.24920	0.114;0.024;0.009	B;B;B	0.20577	0.03;0.007;0.011	T	0.11421	-1.0588	10	0.17369	T	0.5	-10.5316	19.5544	0.95335	0.0:1.0:0.0:0.0	.	100;106;100	B4E0X6;P25786-2;P25786	.;.;PSA1_HUMAN	N	100;100;100;75;106	ENSP00000392242:D100N;ENSP00000379676:D100N;ENSP00000379675:D100N;ENSP00000441166:D75N;ENSP00000414359:D106N	ENSP00000379675:D100N	D	-	1	0	PSMA1	14492570	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.295000	0.65692	2.623000	0.88846	0.591000	0.81541	GAT	PSMA1	-	pfam_Proteasome_sua/b	ENSG00000129084		0.318	PSMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PSMA1	HGNC	protein_coding	OTTHUMT00000386421.3	39	0.00	0	C	NM_002786		14535994	14535994	-1	no_errors	ENST00000418988	ensembl	human	known	69_37n	missense	31	22.50	9	SNP	1.000	T
NELFE	7936	genome.wustl.edu	37	6	31922433	31922433	+	Missense_Mutation	SNP	C	C	T	rs556062290	byFrequency	TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr6:31922433C>T	ENST00000375429.3	-	7	867	c.641G>A	c.(640-642)aGa>aAa	p.R214K	NELFE_ENST00000375425.5_Missense_Mutation_p.R221K|MIR1236_ENST00000408340.1_RNA|NELFE_ENST00000444811.2_Missense_Mutation_p.R184K	NM_002904.5	NP_002895.3	P18615	NELFE_HUMAN	negative elongation factor complex member E	214	30 X 2 AA approximate tandem repeats of R-[DSNE].				gene expression (GO:0010467)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										gtcccgctctctgtctctgtc	0.667																																						dbGAP											0													38.0	37.0	37.0					6																	31922433		2203	4300	6503	-	-	-	SO:0001583	missense	0			M33230	CCDS4730.1	6p21.3	2013-02-12	2013-01-31	2013-01-31	ENSG00000204356	ENSG00000204356		"""RNA binding motif (RRM) containing"""	13974	protein-coding gene	gene with protein product		154040	"""RD RNA-binding protein"", ""RD RNA binding protein"""	RDBP			Standard	XM_006715205		Approved	RD, D6S45, NELF-E, RDP	uc003nyk.3	P18615	OTTHUMG00000031046	ENST00000375429.3:c.641G>A	6.37:g.31922433C>T	ENSP00000364578:p.Arg214Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	A2BE08|B4DUN1|B4DYX9|Q5JP74|Q5JP75|Q96F56|Q9NPK2	Missense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	p.R214K	ENST00000375429.3	37	c.641	CCDS4730.1	6	.	.	.	.	.	.	.	.	.	.	C	7.664	0.685477	0.14973	.	.	ENSG00000204356	ENST00000375429;ENST00000375425;ENST00000444811;ENST00000441998;ENST00000454913;ENST00000436289	T;T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33;-0.33	4.24	4.24	0.50183	.	0.157398	0.40385	N	0.001102	T	0.44973	0.1319	M	0.73217	2.22	0.37069	D	0.898431	P;P;P;P	0.38767	0.646;0.646;0.646;0.646	B;B;B;B	0.31101	0.124;0.124;0.124;0.124	T	0.51325	-0.8720	10	0.30854	T	0.27	-3.3212	9.9336	0.41537	0.0:0.9:0.0:0.1	.	184;209;209;214	B4DUN1;A2ABK1;E9PCL7;P18615	.;.;.;NELFE_HUMAN	K	214;221;184;209;214;209	ENSP00000364578:R214K;ENSP00000364574:R221K;ENSP00000388400:R184K;ENSP00000397914:R209K;ENSP00000409389:R214K;ENSP00000414029:R209K	ENSP00000364574:R221K	R	-	2	0	RDBP	32030412	0.053000	0.20554	0.013000	0.15412	0.011000	0.07611	2.920000	0.48844	2.170000	0.68504	0.591000	0.81541	AGA	RDBP	-	NULL	ENSG00000204356		0.667	NELFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RDBP	HGNC	protein_coding	OTTHUMT00000076047.4	75	0.00	0	C			31922433	31922433	-1	no_errors	ENST00000375429	ensembl	human	known	69_37n	missense	63	12.50	9	SNP	0.742	T
RNPS1	10921	genome.wustl.edu	37	16	2314298	2314298	+	Missense_Mutation	SNP	C	C	A			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr16:2314298C>A	ENST00000565678.1	-	3	651	c.106G>T	c.(106-108)Gat>Tat	p.D36Y	RNPS1_ENST00000566397.1_5'UTR|RNPS1_ENST00000397086.2_Missense_Mutation_p.D36Y|RNPS1_ENST00000569598.2_Intron|RNPS1_ENST00000320225.5_Missense_Mutation_p.D36Y|RNPS1_ENST00000568631.1_Missense_Mutation_p.D36Y|RNPS1_ENST00000567147.1_Missense_Mutation_p.D13Y|RNPS1_ENST00000566458.1_Missense_Mutation_p.D13Y|RNPS1_ENST00000561718.1_5'UTR|RNPS1_ENST00000301730.8_Missense_Mutation_p.D36Y			Q15287	RNPS1_HUMAN	RNA binding protein S1, serine-rich domain	36	Lys-rich.|Necessary for interaction with SRP54, nuclear localization and exon-skipping.|Necessary for interaction with the cleaved p110 isoform of CDC2L1.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)|urinary_tract(1)	9						GACTTCTCATCTGAGCGGTCT	0.547																																						dbGAP											0													123.0	123.0	123.0					16																	2314298		2198	4300	6498	-	-	-	SO:0001583	missense	0			AF015608	CCDS10465.1, CCDS66907.1, CCDS73811.1	16p13.3	2013-02-12	2001-11-28		ENSG00000205937	ENSG00000205937		"""RNA binding motif (RRM) containing"""	10080	protein-coding gene	gene with protein product		606447	"""RNA-binding protein S1, serine-rich domain"""			9580558, 8543184	Standard	XM_005255048		Approved		uc002cpu.3	Q15287	OTTHUMG00000128828	ENST00000565678.1:c.106G>T	16.37:g.2314298C>A	ENSP00000457723:p.Asp36Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1P0|B4DDU8|B4DZU7|B7ZA17|O75308|Q32P25|Q8WY42|Q9NYG3	Missense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	p.D36Y	ENST00000565678.1	37	c.106	CCDS10465.1	16	.	.	.	.	.	.	.	.	.	.	C	28.1	4.894998	0.91962	.	.	ENSG00000205937	ENST00000320225;ENST00000397086;ENST00000301730	T;T;T	0.06528	3.29;3.29;3.29	5.69	5.69	0.88448	.	0.146725	0.64402	D	0.000011	T	0.12220	0.0297	L	0.48642	1.525	0.54753	D	0.999986	P;P	0.45531	0.856;0.86	P;B	0.46825	0.528;0.446	T	0.00270	-1.1860	10	0.66056	D	0.02	-9.8211	17.3031	0.87187	0.0:1.0:0.0:0.0	.	13;36	Q15287-2;Q15287	.;RNPS1_HUMAN	Y	36	ENSP00000315859:D36Y;ENSP00000380275:D36Y;ENSP00000301730:D36Y	ENSP00000301730:D36Y	D	-	1	0	RNPS1	2254299	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.194000	0.77789	2.688000	0.91661	0.551000	0.68910	GAT	RNPS1	-	NULL	ENSG00000205937		0.547	RNPS1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	RNPS1	HGNC	protein_coding	OTTHUMT00000435415.1	114	0.00	0	C	NM_080594		2314298	2314298	-1	no_errors	ENST00000301730	ensembl	human	known	69_37n	missense	110	12.70	16	SNP	1.000	A
RPE	6120	genome.wustl.edu	37	2	210881290	210881290	+	Silent	SNP	G	G	A			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr2:210881290G>A	ENST00000359429.6	+	4	499	c.402G>A	c.(400-402)caG>caA	p.Q134Q	RPE_ENST00000454822.1_Silent_p.Q84Q|RPE_ENST00000445268.1_Silent_p.Q66Q|RPE_ENST00000540255.1_Silent_p.Q134Q|RPE_ENST00000438204.2_Silent_p.Q66Q|RPE_ENST00000435437.2_Silent_p.Q134Q|RPE_ENST00000452025.1_Silent_p.Q134Q|RPE_ENST00000411934.2_Silent_p.Q66Q|RPE_ENST00000354506.6_Silent_p.Q126Q|RPE_ENST00000429921.1_Silent_p.Q84Q|RPE_ENST00000429907.1_Silent_p.Q66Q|RPE_ENST00000436630.2_Silent_p.Q84Q	NM_199229.1	NP_954699.1	Q96AT9	RPE_HUMAN	ribulose-5-phosphate-3-epimerase	134					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|ribulose-phosphate 3-epimerase activity (GO:0004750)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	9				Epithelial(149;0.00241)|Lung(261;0.041)|all cancers(144;0.0429)|LUSC - Lung squamous cell carcinoma(261;0.0431)		GGGCTAATCAGATAGATATGG	0.418																																						dbGAP											0													120.0	115.0	117.0					2																	210881290		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS2388.1, CCDS42810.1, CCDS63107.1, CCDS63108.1	2q32-q33.3	2012-10-02			ENSG00000197713	ENSG00000197713	5.1.3.1		10293	protein-coding gene	gene with protein product		180480					Standard	NM_199229		Approved		uc002vdn.4	Q96AT9	OTTHUMG00000154690	ENST00000359429.6:c.402G>A	2.37:g.210881290G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K4S0|B4E016|C9JPQ7|O43767|Q53TV9|Q8N215|Q96N34|Q9BSB5	Silent	SNP	pfam_Ribul_P_3_epim-like,superfamily_RibuloseP-bd_barrel,tigrfam_Ribul_P_3_epim-like	p.Q134	ENST00000359429.6	37	c.402	CCDS2388.1	2																																																																																			RPE	-	pfam_Ribul_P_3_epim-like,superfamily_RibuloseP-bd_barrel,tigrfam_Ribul_P_3_epim-like	ENSG00000197713		0.418	RPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPE	HGNC	protein_coding	OTTHUMT00000336574.2	116	0.00	0	G	NM_006916		210881290	210881290	+1	no_errors	ENST00000359429	ensembl	human	known	69_37n	silent	128	18.99	30	SNP	0.994	A
SBF2	81846	genome.wustl.edu	37	11	10011089	10011089	+	Missense_Mutation	SNP	C	C	G			TCGA-AC-A2FO-01A-11D-A17W-09	TCGA-AC-A2FO-11A-12D-A17W-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	588bf255-b3bd-4247-9d39-9c1172260e5e	a62dd4a6-868e-44fd-a9ae-ff8140550aaa	g.chr11:10011089C>G	ENST00000256190.8	-	13	1487	c.1350G>C	c.(1348-1350)aaG>aaC	p.K450N		NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	450					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)		GCTTTATCATCTTCACTGGGT	0.284																																						dbGAP											0													102.0	105.0	104.0					11																	10011089		2200	4293	6493	-	-	-	SO:0001583	missense	0			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.1350G>C	11.37:g.10011089C>G	ENSP00000256190:p.Lys450Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Missense_Mutation	SNP	pfam_SBF2,pfam_DENN_dom,pfam_uDENN_dom,pfam_Myotub-related,pfam_dDENN_dom,pfam_Pleckstrin_homology,pfam_GRAM,smart_uDENN_dom,smart_DENN_dom,smart_dDENN_dom,smart_GRAM,smart_Pleckstrin_homology,pfscan_DENN_dom,pfscan_uDENN_dom,pfscan_dDENN_dom,pfscan_Pleckstrin_homology	p.K450N	ENST00000256190.8	37	c.1350	CCDS31427.1	11	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.66|15.66	2.899895|2.899895	0.52227|0.52227	.|.	.|.	ENSG00000133812|ENSG00000133812	ENST00000420722|ENST00000256190	.|D	.|0.86030	.|-2.06	6.17|6.17	2.87|2.87	0.33458|0.33458	.|.	.|0.105487	.|0.64402	.|N	.|0.000006	T|T	0.77552|0.77552	0.4147|0.4147	L|L	0.49350|0.49350	1.555|1.555	0.53005|0.53005	D|D	0.999968|0.999968	.|B	.|0.24426	.|0.103	.|B	.|0.24848	.|0.056	T|T	0.67511|0.67511	-0.5652|-0.5652	5|10	.|0.22706	.|T	.|0.39	.|.	6.7588|6.7588	0.23528|0.23528	0.0:0.5587:0.0:0.4413|0.0:0.5587:0.0:0.4413	.|.	.|450	.|Q86WG5	.|MTMRD_HUMAN	H|N	57|450	.|ENSP00000256190:K450N	.|ENSP00000256190:K450N	D|K	-|-	1|3	0|2	SBF2|SBF2	9967665|9967665	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.857000|0.857000	0.48899|0.48899	1.160000|1.160000	0.31761|0.31761	0.866000|0.866000	0.35629|0.35629	0.655000|0.655000	0.94253|0.94253	GAT|AAG	SBF2	-	NULL	ENSG00000133812		0.284	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SBF2	HGNC	protein_coding	OTTHUMT00000386911.2	208	0.00	0	C	NM_030962		10011089	10011089	-1	no_errors	ENST00000256190	ensembl	human	known	69_37n	missense	129	12.84	19	SNP	1.000	G
