#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
RERE	473	broad.mit.edu	37	1	8424241	8424242	+	Frame_Shift_Ins	INS	-	-	T			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr1:8424241_8424242insT	ENST00000337907.3	-	16	2248_2249	c.1614_1615insA	c.(1612-1617)aaatacfs	p.Y539fs	RERE_ENST00000400907.2_Intron|RERE_ENST00000377464.1_Frame_Shift_Ins_p.Y271fs|RERE_ENST00000476556.1_5'UTR|RERE_ENST00000400908.2_Frame_Shift_Ins_p.Y539fs|RERE_ENST00000460659.1_5'Flank	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	539					chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		AGCTCACCGTATTTCTTGAAGT	0.569																																						uc001ape.2																			0				ovary(1)|central_nervous_system(1)	2						c.(1612-1617)AAATACfs		atrophin-1 like protein isoform a																																				SO:0001589	frameshift_variant	473				multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr1:8424241_8424242insT	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.1615dupA	1.37:g.8424244_8424244dupT	ENSP00000338629:p.Tyr539fs					RERE_uc001apf.2_Frame_Shift_Ins_p.K538fs|RERE_uc010nzx.1_Frame_Shift_Ins_p.K270fs|RERE_uc001apd.2_5'UTR	p.K538fs	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)	16	2424_2425	-	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)	538_539					O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Frame_Shift_Ins	INS	ENST00000337907.3	37	c.1614_1615insA	CCDS95.1																																																																																				0.569	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
MSH4	4438	broad.mit.edu	37	1	76288094	76288094	+	Splice_Site	SNP	G	G	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr1:76288094G>A	ENST00000263187.3	+	7	1094	c.990G>A	c.(988-990)agG>agA	p.R330R		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	330					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						GTTTTGAAAGGAATAATCACA	0.308								Mismatch excision repair (MMR)																														uc001dhd.1																			0				lung(3)|ovary(2)	5						c.(988-990)AGG>AGA	MMR	mutS homolog 4							78.0	81.0	80.0					1																	76288094		2203	4296	6499	SO:0001630	splice_region_variant	4438				chiasma assembly|homologous chromosome segregation|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding	g.chr1:76288094G>A	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"""mutS (E. coli) homolog 4"", ""mutS homolog 4 (E. coli)"""			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.990-1G>A	1.37:g.76288094G>A							p.R330R	NM_002440	NP_002431	O15457	MSH4_HUMAN			7	1031	+			330					Q5T4U6|Q8NEB3|Q9UNP8	Silent	SNP	ENST00000263187.3	37	c.990G>A	CCDS670.1																																																																																				0.308	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	Silent
RPL5	6125	broad.mit.edu	37	1	93303161	93303161	+	Missense_Mutation	SNP	T	T	C			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr1:93303161T>C	ENST00000370321.3	+	6	766	c.676T>C	c.(676-678)Tac>Cac	p.Y226H	SNORA66_ENST00000515986.1_RNA|SNORD21_ENST00000383953.1_RNA	NM_000969.3	NP_000960.2	P46777	RL5_HUMAN	ribosomal protein L5	226					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	5S rRNA binding (GO:0008097)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)		GTTCTCTCAATACATAAAGAA	0.368																																						uc001doz.2																			0					0						c.(676-678)TAC>CAC		ribosomal protein L5							27.0	26.0	27.0					1																	93303161		2196	4279	6475	SO:0001583	missense	6125				endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	5S rRNA binding|protein binding|structural constituent of ribosome	g.chr1:93303161T>C	U14966	CCDS741.1	1p22.1	2014-06-13			ENSG00000122406	ENSG00000122406		"""L ribosomal proteins"""	10360	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 135"""	603634				7937132, 7772601	Standard	NM_000969		Approved	L5, PPP1R135	uc001doz.3	P46777	OTTHUMG00000010899	ENST00000370321.3:c.676T>C	1.37:g.93303161T>C	ENSP00000359345:p.Tyr226His					FAM69A_uc001dpc.2_Intron|RPL5_uc001dpa.2_RNA|RPL5_uc001dpb.2_Missense_Mutation_p.Y176H|RPL5_uc001dpd.2_Missense_Mutation_p.Y27H	p.Y226H	NM_000969	NP_000960	P46777	RL5_HUMAN		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)	6	754	+		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)	226					Q32LZ3|Q53HH6|Q9H3F4	Missense_Mutation	SNP	ENST00000370321.3	37	c.676T>C	CCDS741.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.276193	0.80580	.	.	ENSG00000122406	ENST00000432788;ENST00000370321	T	0.65364	-0.15	5.06	5.06	0.68205	.	0.057817	0.64402	D	0.000001	T	0.81442	0.4823	H	0.94734	3.575	0.80722	D	1	D;D	0.61697	0.99;0.99	D;D	0.70016	0.967;0.967	D	0.87185	0.2230	10	0.87932	D	0	.	15.102	0.72288	0.0:0.0:0.0:1.0	.	226;226	A2RUM7;P46777	.;RL5_HUMAN	H	176;226	ENSP00000359345:Y226H	ENSP00000359345:Y226H	Y	+	1	0	RPL5	93075749	1.000000	0.71417	0.893000	0.35052	0.863000	0.49368	7.785000	0.85724	2.017000	0.59298	0.533000	0.62120	TAC		0.368	RPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030058.2	NM_000969	
SCYL3	57147	broad.mit.edu	37	1	169833511	169833511	+	Splice_Site	DEL	T	T	-			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr1:169833511delT	ENST00000367770.1	-	8	1001	c.954delA	c.(952-954)aaa>aa	p.K318fs	SCYL3_ENST00000470238.1_5'UTR|SCYL3_ENST00000367772.4_Splice_Site_p.K318fs|SCYL3_ENST00000367771.6_Splice_Site_p.K318fs			Q8IZE3	PACE1_HUMAN	SCY1-like 3 (S. cerevisiae)	318					cell migration (GO:0016477)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AGCATTCACCTTTTTTGGGGC	0.393																																						uc001ggs.2																			0				ovary(1)|skin(1)	2						c.(952-954)AAAfs		SCY1-like 3 isoform 2							92.0	94.0	94.0					1																	169833511		2203	4300	6503	SO:0001630	splice_region_variant	57147				cell migration	Golgi apparatus|lamellipodium	ATP binding|protein binding|protein kinase activity	g.chr1:169833511delT	BC014662	CCDS1286.1, CCDS1287.1	1q24.2	2008-02-05			ENSG00000000457	ENSG00000000457			19285	protein-coding gene	gene with protein product	"""ezrin-binding partner PACE-1"""	608192				12651155	Standard	NM_020423		Approved	PACE-1, PACE1	uc001ggs.3	Q8IZE3	OTTHUMG00000035941	ENST00000367770.1:c.955+1A>-	1.37:g.169833511delT						SCYL3_uc010plw.1_5'UTR|SCYL3_uc001ggt.2_Frame_Shift_Del_p.K318fs|SCYL3_uc001ggu.2_RNA	p.K318fs	NM_181093	NP_851607	Q8IZE3	PACE1_HUMAN			9	1152	-	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)		318			HEAT 2.		A8K8Z2|Q5THA6|Q5THA8|Q8IZN9|Q96C56|Q9UBK6	Frame_Shift_Del	DEL	ENST00000367770.1	37	c.954delA	CCDS1287.1																																																																																				0.393	SCYL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087550.4	NM_181093	Frame_Shift_Del
RAG2	5897	broad.mit.edu	37	11	36615451	36615451	+	Missense_Mutation	SNP	G	G	C	rs149769148		TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr11:36615451G>C	ENST00000311485.3	-	2	429	c.268C>G	c.(268-270)Caa>Gaa	p.Q90E	C11orf74_ENST00000446510.2_5'Flank|C11orf74_ENST00000347206.4_5'Flank|C11orf74_ENST00000534635.1_5'Flank|RAG2_ENST00000528428.1_5'Flank|C11orf74_ENST00000334307.5_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	90					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				ATGATGTATTGATGCTTTTCA	0.413									Familial Hemophagocytic Lymphohistiocytosis																													uc001mwv.3																			0				skin(3)|ovary(1)|pancreas(1)	5						c.(268-270)CAA>GAA		recombination activating gene 2		G	GLU/GLN	0,4404		0,0,2202	156.0	158.0	157.0		268	3.8	1.0	11	dbSNP_134	157	1,8595	1.2+/-3.3	0,1,4297	no	missense	RAG2	NM_000536.3	29	0,1,6499	CC,CG,GG		0.0116,0.0,0.0077	benign	90/528	36615451	1,12999	2202	4298	6500	SO:0001583	missense	5897	Familial_Hemophagocytic_Lymphohistiocytosis	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	chromatin modification|pre-B cell allelic exclusion|somatic diversification of immunoglobulins|T cell differentiation in thymus|V(D)J recombination	nucleus	chromatin binding|DNA binding|endonuclease activity|methylated histone residue binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-4,5-bisphosphate binding|zinc ion binding	g.chr11:36615451G>C	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.268C>G	11.37:g.36615451G>C	ENSP00000308620:p.Gln90Glu					C11orf74_uc010rfd.1_5'Flank|C11orf74_uc001mww.1_5'Flank|C11orf74_uc001mwx.1_5'Flank|C11orf74_uc001mwy.1_5'Flank|C11orf74_uc001mwz.1_5'Flank|C11orf74_uc010rfe.1_5'Flank	p.Q90E	NM_000536	NP_000527	P55895	RAG2_HUMAN			2	456	-	all_lung(20;0.226)	all_hematologic(20;0.00756)	90					A8K9E9|Q8TBL4	Missense_Mutation	SNP	ENST00000311485.3	37	c.268C>G	CCDS7903.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	11.64	1.700138	0.30142	0.0	1.16E-4	ENSG00000175097	ENST00000311485;ENST00000529083	T;T	0.73575	-0.76;-0.73	5.73	3.79	0.43588	Galactose oxidase/kelch, beta-propeller (1);Kelch-type beta propeller (1);	0.259107	0.39985	N	0.001208	T	0.80984	0.4729	M	0.92219	3.285	0.39817	D	0.97278	B	0.10296	0.003	B	0.13407	0.009	T	0.80167	-0.1495	10	0.66056	D	0.02	-25.9494	16.1002	0.81166	0.0:0.2533:0.7467:0.0	.	90	P55895	RAG2_HUMAN	E	90	ENSP00000308620:Q90E;ENSP00000436327:Q90E	ENSP00000308620:Q90E	Q	-	1	0	RAG2	36572027	0.991000	0.36638	0.984000	0.44739	0.888000	0.51559	2.473000	0.45145	0.704000	0.31869	0.650000	0.86243	CAA		0.413	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536	
KDELC2	143888	broad.mit.edu	37	11	108361783	108361783	+	Missense_Mutation	SNP	C	C	T	rs201945088		TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr11:108361783C>T	ENST00000323468.5	-	2	379	c.314G>A	c.(313-315)aGg>aAg	p.R105K	KDELC2_ENST00000434945.2_Missense_Mutation_p.R49K|KDELC2_ENST00000375648.1_Missense_Mutation_p.R49K	NM_153705.4	NP_714916.3	Q7Z4H8	KDEL2_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 2	105						endoplasmic reticulum (GO:0005783)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;6.93e-06)|BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|all cancers(92;0.00016)|OV - Ovarian serous cystadenocarcinoma(223;0.132)|Colorectal(284;0.14)		TTCATACATCCTATATCTCAT	0.388																																						uc001pkj.2																			0				ovary(1)	1						c.(313-315)AGG>AAG		KDEL (Lys-Asp-Glu-Leu) containing 2 precursor							103.0	100.0	101.0					11																	108361783		1924	4139	6063	SO:0001583	missense	143888					endoplasmic reticulum lumen		g.chr11:108361783C>T	AF533708	CCDS41711.1	11q32	2010-11-18			ENSG00000178202	ENSG00000178202			28496	protein-coding gene	gene with protein product						12975309	Standard	NM_153705		Approved	MGC33424	uc001pkj.2	Q7Z4H8	OTTHUMG00000166535	ENST00000323468.5:c.314G>A	11.37:g.108361783C>T	ENSP00000315386:p.Arg105Lys					KDELC2_uc001pki.2_Missense_Mutation_p.R49K	p.R105K	NM_153705	NP_714916	Q7Z4H8	KDEL2_HUMAN		Epithelial(105;6.93e-06)|BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|all cancers(92;0.00016)|OV - Ovarian serous cystadenocarcinoma(223;0.132)|Colorectal(284;0.14)	2	380	-		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)	105			Filamin.		Q6UWW2|Q6ZUM9|Q8N7L8|Q8NE24	Missense_Mutation	SNP	ENST00000323468.5	37	c.314G>A	CCDS41711.1	.	.	.	.	.	.	.	.	.	.	C	10.90	1.481721	0.26598	.	.	ENSG00000178202	ENST00000323468;ENST00000434945;ENST00000375648	T;T;T	0.22134	1.97;2.27;2.54	5.05	4.07	0.47477	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.24198	0.0586	L	0.42686	1.345	0.49915	D	0.999834	B;B	0.32893	0.02;0.389	B;B	0.43478	0.135;0.421	T	0.02238	-1.1190	10	0.14252	T	0.57	-18.298	14.0667	0.64834	0.0:0.9162:0.0:0.0838	.	105;49	Q7Z4H8;Q7Z4H8-2	KDEL2_HUMAN;.	K	105;49;49	ENSP00000315386:R105K;ENSP00000413429:R49K;ENSP00000364799:R49K	ENSP00000315386:R105K	R	-	2	0	KDELC2	107866993	1.000000	0.71417	0.153000	0.22517	0.313000	0.28021	5.579000	0.67457	2.640000	0.89533	0.561000	0.74099	AGG		0.388	KDELC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390273.1	NM_153705	
ESAM	90952	broad.mit.edu	37	11	124623728	124623728	+	Silent	SNP	A	A	C			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr11:124623728A>C	ENST00000278927.5	-	7	1116	c.987T>G	c.(985-987)ggT>ggG	p.G329G	ESAM_ENST00000442070.2_Intron|VSIG2_ENST00000326621.5_5'Flank|VSIG2_ENST00000403470.1_5'Flank	NM_138961.2	NP_620411.2	Q96AP7	ESAM_HUMAN	endothelial cell adhesion molecule	329					blood coagulation (GO:0007596)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)|single organismal cell-cell adhesion (GO:0016337)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.022)		GGGTCAATGCACCAGGCCTGG	0.647																																						uc001qav.3																			0					0						c.(985-987)GGT>GGG		endothelial cell adhesion molecule precursor							58.0	67.0	64.0					11																	124623728		2201	4299	6500	SO:0001819	synonymous_variant	90952				blood coagulation|leukocyte migration	adherens junction|integral to membrane|tight junction		g.chr11:124623728A>C	AK075396	CCDS8453.1	11q24.2	2013-01-29			ENSG00000149564	ENSG00000149564		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17474	protein-coding gene	gene with protein product		614281				11279107, 11906820	Standard	NM_138961		Approved	W117m	uc001qav.4	Q96AP7	OTTHUMG00000151986	ENST00000278927.5:c.987T>G	11.37:g.124623728A>C						VSIG2_uc001qas.2_5'Flank|VSIG2_uc001qat.2_5'Flank|ESAM_uc010sao.1_Intron|ESAM_uc001qau.3_Silent_p.G256G|ESAM_uc001qaw.3_RNA|ESAM_uc001qax.3_RNA|ESAM_uc009zbi.2_Missense_Mutation_p.V328G	p.G329G	NM_138961	NP_620411	Q96AP7	ESAM_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.022)	7	1160	-	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	329			Cytoplasmic (Potential).		B4DVN8|Q96T50	Silent	SNP	ENST00000278927.5	37	c.987T>G	CCDS8453.1																																																																																				0.647	ESAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324686.1	NM_138961	
ANKRD33	341405	broad.mit.edu	37	12	52284586	52284586	+	Missense_Mutation	SNP	C	C	T	rs200291062		TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr12:52284586C>T	ENST00000340970.4	+	5	852	c.481C>T	c.(481-483)Cgg>Tgg	p.R161W	ANKRD33_ENST00000538991.1_Missense_Mutation_p.R92W|ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000301190.6_Missense_Mutation_p.R286W			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	161					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.0969)		ACTCCTAGAACGGCTGCAGGC	0.662																																						uc001rzf.3																			0					0						c.(481-483)CGG>TGG		ankyrin repeat domain 33 isoform 1		C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	25.0	24.0	24.0		481,856	0.1	0.6	12		24	4,8590		0,4,4293	yes	missense,missense	ANKRD33	NM_001130015.1,NM_182608.3	101,101	0,4,6496	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging,probably-damaging	161/273,286/453	52284586	4,12996	2203	4297	6500	SO:0001583	missense	341405							g.chr12:52284586C>T		CCDS8815.1, CCDS44892.1	12q13.13	2013-01-10	2005-01-07	2005-01-07		ENSG00000167612		"""Ankyrin repeat domain containing"""	13788	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 7"""	C12orf7		20026326	Standard	NM_182608		Approved	DKFZp686O1689, PANKY	uc001rzd.3	Q7Z3H0	OTTHUMG00000169506	ENST00000340970.4:c.481C>T	12.37:g.52284586C>T	ENSP00000344690:p.Arg161Trp					ANKRD33_uc001rzh.3_3'UTR|ANKRD33_uc001rzd.2_Missense_Mutation_p.R286W|ANKRD33_uc001rze.2_Missense_Mutation_p.R182W|ANKRD33_uc001rzg.3_Missense_Mutation_p.R88W|ANKRD33_uc001rzi.3_Missense_Mutation_p.R161W	p.R161W	NM_001130015	NP_001123487	Q7Z3H0	ANR33_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.0969)	5	1060	+			161					Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Missense_Mutation	SNP	ENST00000340970.4	37	c.481C>T	CCDS44892.1	.	.	.	.	.	.	.	.	.	.	C	14.05	2.419121	0.42918	0.0	4.65E-4	ENSG00000167612	ENST00000301190;ENST00000538991;ENST00000340970	T;T;T	0.24908	1.93;1.83;2.28	4.7	0.0507	0.14294	.	0.080339	0.47455	D	0.000234	T	0.39655	0.1086	L	0.55481	1.735	0.21473	N	0.999672	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74674	0.965;0.984;0.977	T	0.22836	-1.0205	10	0.37606	T	0.19	-7.9632	11.629	0.51162	0.7308:0.2692:0.0:0.0	.	161;92;286	Q7Z3H0;Q0VAA8;Q7Z3H0-2	ANR33_HUMAN;.;.	W	286;92;161	ENSP00000301190:R286W;ENSP00000443722:R92W;ENSP00000344690:R161W	ENSP00000301190:R286W	R	+	1	2	ANKRD33	50570853	0.279000	0.24239	0.605000	0.28930	0.607000	0.37147	0.456000	0.21859	0.192000	0.20272	0.561000	0.74099	CGG		0.662	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
FOXG1	2290	broad.mit.edu	37	14	29236624	29236626	+	In_Frame_Del	DEL	CAC	CAC	-			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr14:29236624_29236626delCAC	ENST00000313071.4	+	1	338_340	c.139_141delCAC	c.(139-141)cacdel	p.H57del	RP11-966I7.1_ENST00000551395.1_RNA|RP11-966I7.1_ENST00000546560.1_RNA|FOXG1_ENST00000382535.3_In_Frame_Del_p.H57del|RP11-966I7.1_ENST00000549487.1_RNA	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	57	His-rich.				aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		ccacccccagcaccaccaccacc	0.744																																						uc001wqe.2																			0				ovary(2)|lung(2)	4						c.(139-141)CACdel		forkhead box G1				130,3588		4,122,1733						1.2	0.0			27	280,6952		9,262,3345	no	coding	FOXG1	NM_005249.3		13,384,5078	A1A1,A1R,RR		3.8717,3.4965,3.7443				410,10540				SO:0001651	inframe_deletion	2290				axon midline choice point recognition|central nervous system neuron development|dorsal/ventral pattern formation|embryo development ending in birth or egg hatching|hindbrain development|inner ear morphogenesis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|nonmotile primary cilium assembly|nose development|positive regulation of cell cycle|positive regulation of neuroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of mitotic cell cycle|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding	g.chr14:29236624_29236626delCAC		CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"""Forkhead boxes"""	3811	protein-coding gene	gene with protein product		164874	"""forkhead box G1B"", ""forkhead box G1C"", ""forkhead box G1A"""	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.139_141delCAC	14.37:g.29236633_29236635delCAC	ENSP00000339004:p.His57del						p.H57del	NM_005249	NP_005240	P55316	FOXG1_HUMAN	LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)	1	338_340	+			57			His-rich.		A6NFY2|P55315|Q14488|Q86XT7	In_Frame_Del	DEL	ENST00000313071.4	37	c.139_141delCAC	CCDS9636.1																																																																																				0.744	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3		
IGDCC3	9543	broad.mit.edu	37	15	65621380	65621380	+	Missense_Mutation	SNP	T	T	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr15:65621380T>A	ENST00000327987.4	-	14	2563	c.2312A>T	c.(2311-2313)gAg>gTg	p.E771V	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	771					neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AGCCGTGGCCTCTGTGGTCTT	0.716																																						uc002aos.2																			0				ovary(3)	3						c.(2311-2313)GAG>GTG		putative neuronal cell adhesion molecule							16.0	21.0	19.0					15																	65621380		2200	4299	6499	SO:0001583	missense	9543							g.chr15:65621380T>A	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9700	protein-coding gene	gene with protein product		604184	"""putative neuronal cell adhesion molecule"""	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.2312A>T	15.37:g.65621380T>A	ENSP00000332773:p.Glu771Val					IGDCC3_uc002aor.1_Missense_Mutation_p.E57V	p.E771V	NM_004884	NP_004875	Q8IVU1	IGDC3_HUMAN			14	2564	-			771			Cytoplasmic (Potential).		O95215	Missense_Mutation	SNP	ENST00000327987.4	37	c.2312A>T	CCDS10205.1	.	.	.	.	.	.	.	.	.	.	T	6.693	0.496552	0.12762	.	.	ENSG00000174498	ENST00000327987;ENST00000443278	T	0.66815	-0.23	.	.	.	.	0.542417	0.15481	N	0.260109	T	0.49406	0.1555	L	0.27053	0.805	0.09310	N	1	.	.	.	.	.	.	T	0.36792	-0.9733	6	0.28530	T	0.3	-10.9933	.	.	.	.	771	Q8IVU1	IGDC3_HUMAN	V	771;594	ENSP00000332773:E771V	ENSP00000332773:E771V	E	-	2	0	IGDCC3	63408433	0.500000	0.26091	0.025000	0.17156	0.029000	0.11900	0.077000	0.14738	0.056000	0.16144	0.055000	0.15244	GAG		0.716	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884	
RBBP6	5930	broad.mit.edu	37	16	24581255	24581256	+	Frame_Shift_Ins	INS	-	-	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr16:24581255_24581256insA	ENST00000319715.4	+	17	3676_3677	c.3244_3245insA	c.(3244-3246)gaafs	p.E1082fs	RBBP6_ENST00000381039.3_Intron|RBBP6_ENST00000348022.2_Frame_Shift_Ins_p.E1048fs	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1082	Interaction with RB1. {ECO:0000250}.				embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TCAGAAGGATGAAAAAATCACT	0.406																																						uc002dmh.2																			0				ovary(3)|pancreas(1)	4						c.(3244-3246)GAAfs		retinoblastoma-binding protein 6 isoform 1																																				SO:0001589	frameshift_variant	5930				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr16:24581255_24581256insA		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.3250dupA	16.37:g.24581261_24581261dupA	ENSP00000317872:p.Glu1082fs					RBBP6_uc010vcb.1_Frame_Shift_Ins_p.E949fs|RBBP6_uc002dmi.2_Frame_Shift_Ins_p.E1048fs|RBBP6_uc010bxr.2_Intron|RBBP6_uc002dmk.2_Frame_Shift_Ins_p.E915fs	p.E1082fs	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN		GBM - Glioblastoma multiforme(48;0.0518)	17	4284_4285	+			1082			Interaction with RB1 (By similarity).		Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Frame_Shift_Ins	INS	ENST00000319715.4	37	c.3244_3245insA	CCDS10621.1																																																																																				0.406	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
CES3	23491	broad.mit.edu	37	16	66997813	66997813	+	Missense_Mutation	SNP	C	C	T	rs148620443		TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr16:66997813C>T	ENST00000303334.4	+	4	606	c.535C>T	c.(535-537)Cgc>Tgc	p.R179C	CES3_ENST00000394037.1_Missense_Mutation_p.R179C|RP11-361L15.4_ENST00000566869.1_RNA	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	179						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		AGTCCAGTACCGCCTTGGGGT	0.607													c|||	1	0.000199681	0.0	0.0	5008	,	,		19924	0.0		0.001	False		,,,				2504	0.0					uc002eqt.2																			0				ovary(3)|central_nervous_system(2)	5						c.(535-537)CGC>TGC		carboxylesterase 3 precursor		C	CYS/ARG,CYS/ARG	2,4398	4.2+/-10.8	0,2,2198	138.0	122.0	127.0		535,535	2.0	0.8	16	dbSNP_134	127	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense	CES3	NM_001185177.1,NM_024922.5	180,180	0,9,6491	TT,TC,CC		0.0814,0.0455,0.0692	probably-damaging,probably-damaging	179/569,179/572	66997813	9,12991	2200	4300	6500	SO:0001583	missense	23491					endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity	g.chr16:66997813C>T	AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"""Carboxylesterases"""	1865	protein-coding gene	gene with protein product	"""esterase 31"", ""brain carboxylesterase BR3"""	605279	"""carboxylesterase 3 (brain)"""			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.535C>T	16.37:g.66997813C>T	ENSP00000304782:p.Arg179Cys					CES3_uc010cdz.2_Missense_Mutation_p.R179C|CES3_uc010cea.2_RNA	p.R179C	NM_024922	NP_079198	Q6UWW8	EST3_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)	4	608	+		Ovarian(137;0.0563)	179					B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Missense_Mutation	SNP	ENST00000303334.4	37	c.535C>T	CCDS10826.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.10	3.547802	0.65311	4.55E-4	8.14E-4	ENSG00000172828	ENST00000303334;ENST00000394037	D;D	0.90788	-2.73;-2.73	4.15	2.02	0.26589	Carboxylesterase, type B (1);	0.198539	0.25319	N	0.031529	D	0.96294	0.8791	H	0.98664	4.295	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94029	0.7299	10	0.87932	D	0	.	5.0707	0.14606	0.345:0.5464:0.0:0.1086	.	179	Q6UWW8	EST3_HUMAN	C	179	ENSP00000304782:R179C;ENSP00000377602:R179C	ENSP00000304782:R179C	R	+	1	0	CES3	65555314	0.998000	0.40836	0.784000	0.31847	0.026000	0.11368	1.740000	0.38228	1.086000	0.41228	0.609000	0.83330	CGC		0.607	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922	
SSTR2	6752	broad.mit.edu	37	17	71166297	71166297	+	Missense_Mutation	SNP	T	T	C			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr17:71166297T>C	ENST00000357585.2	+	2	1208	c.839T>C	c.(838-840)gTc>gCc	p.V280A	RP11-143K11.5_ENST00000580671.1_RNA|SSTR2_ENST00000315332.2_Missense_Mutation_p.V280A	NM_001050.2	NP_001041.1	P30874	SSR2_HUMAN	somatostatin receptor 2	280					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|peristalsis (GO:0030432)|regulation of muscle contraction (GO:0006937)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|somatostatin receptor activity (GO:0004994)			endometrium(2)|large_intestine(5)|lung(2)|prostate(2)	11			LUSC - Lung squamous cell carcinoma(166;0.197)		Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	GTTTCTTCCGTCTCCATGGCC	0.512																																						uc002jje.2																			0					0						c.(838-840)GTC>GCC		somatostatin receptor 2							213.0	175.0	188.0					17																	71166297		2203	4300	6503	SO:0001583	missense	6752				digestion|negative regulation of cell proliferation|response to nutrient	integral to plasma membrane	PDZ domain binding|somatostatin receptor activity	g.chr17:71166297T>C		CCDS11691.1	17q24	2012-08-08				ENSG00000180616		"""GPCR / Class A : Somatostatin receptors"""	11331	protein-coding gene	gene with protein product		182452				8449518	Standard	NM_001050		Approved		uc002jje.3	P30874		ENST00000357585.2:c.839T>C	17.37:g.71166297T>C	ENSP00000350198:p.Val280Ala						p.V280A	NM_001050	NP_001041	P30874	SSR2_HUMAN	LUSC - Lung squamous cell carcinoma(166;0.197)		2	1199	+			280			Extracellular (Potential).		A8K3Y0|B2R9P7|Q4VBP0|Q96GE0|Q96TF2|Q9BWH1	Missense_Mutation	SNP	ENST00000357585.2	37	c.839T>C	CCDS11691.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.576464	0.45902	.	.	ENSG00000180616	ENST00000357585;ENST00000315332	T;T	0.36520	1.25;1.25	5.49	5.49	0.81192	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.40815	0.1132	L	0.28014	0.82	0.80722	D	1	P	0.36171	0.541	P	0.49953	0.627	T	0.24440	-1.0160	10	0.32370	T	0.25	.	15.2552	0.73579	0.0:0.0:0.0:1.0	.	280	P30874	SSR2_HUMAN	A	280	ENSP00000350198:V280A;ENSP00000326616:V280A	ENSP00000326616:V280A	V	+	2	0	SSTR2	68677892	1.000000	0.71417	0.465000	0.27155	0.496000	0.33645	8.036000	0.88901	2.084000	0.62774	0.533000	0.62120	GTC		0.512	SSTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441633.1		
CDH19	28513	broad.mit.edu	37	18	64178924	64178925	+	Splice_Site	INS	-	-	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr18:64178924_64178925insA	ENST00000262150.2	-	10	1751		c.e10-2		CDH19_ENST00000540086.1_Intron	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2						branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				CTGAATTACCTAAAAAAAAAGG	0.317																																						uc002lkc.1																			0				ovary(1)|skin(1)	2						c.e10-1		cadherin 19, type 2 preproprotein				8,4256		0,8,2124						4.9	1.0			66	12,8234		0,12,4111	no	splice-3	CDH19	NM_021153.2		0,20,6235	A1A1,A1R,RR		0.1455,0.1876,0.1599				20,12490				SO:0001630	splice_region_variant	28513				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr18:64178924_64178925insA	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"""Cadherins / Major cadherins"""	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000262150.2:c.1459-2->T	18.37:g.64178933_64178933dupA						CDH19_uc010dql.1_Splice_Site|CDH19_uc010xey.1_Intron	p.V487_splice	NM_021153	NP_066976	Q9H159	CAD19_HUMAN			10	1597	-		Esophageal squamous(42;0.0132)						O15098	Splice_Site	INS	ENST00000262150.2	37	c.1459_splice	CCDS11994.1																																																																																				0.317	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153	Intron
ZNF516	9658	broad.mit.edu	37	18	74091275	74091275	+	Missense_Mutation	SNP	G	G	A	rs370362208		TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr18:74091275G>A	ENST00000443185.2	-	4	3112	c.2795C>T	c.(2794-2796)aCg>aTg	p.T932M	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	932					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T932M(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		GACGGTGGGCGTAGGGGTGGC	0.726																																						uc010dqx.1																			1	Substitution - Missense(1)		central_nervous_system(1)	ovary(1)	1						c.(2794-2796)ACG>ATG		zinc finger protein 516		G	MET/THR	0,3554		0,0,1777	14.0	18.0	17.0		2795	3.2	0.2	18		17	2,7742		0,2,3870	no	missense	ZNF516	NM_014643.3	81	0,2,5647	AA,AG,GG		0.0258,0.0,0.0177	possibly-damaging	932/1164	74091275	2,11296	1777	3872	5649	SO:0001583	missense	9658				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr18:74091275G>A	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.2795C>T	18.37:g.74091275G>A	ENSP00000394757:p.Thr932Met					ZNF516_uc002lme.2_RNA|ZNF516_uc002lmd.2_RNA	p.T932M	NM_014643	NP_055458	Q92618	ZN516_HUMAN		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)	3	3030	-		Prostate(75;0.0869)|Esophageal squamous(42;0.129)	932						Missense_Mutation	SNP	ENST00000443185.2	37	c.2795C>T		.	.	.	.	.	.	.	.	.	.	G	10.43	1.346879	0.24426	0.0	2.58E-4	ENSG00000101493	ENST00000443185	T	0.10960	2.82	4.13	3.25	0.37280	.	0.353403	0.25968	N	0.027147	T	0.10680	0.0261	.	.	.	0.18873	N	0.999982	P	0.52316	0.952	B	0.40477	0.33	T	0.11060	-1.0603	9	0.87932	D	0	-9.6177	12.7492	0.57298	0.0:0.1645:0.8354:0.0	.	932	Q92618	ZN516_HUMAN	M	932	ENSP00000394757:T932M	ENSP00000394757:T932M	T	-	2	0	ZNF516	72220263	0.655000	0.27376	0.171000	0.22900	0.545000	0.35147	2.655000	0.46707	1.088000	0.41272	0.491000	0.48974	ACG		0.726	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
ZNF135	7694	broad.mit.edu	37	19	58578313	58578313	+	Missense_Mutation	SNP	C	C	T			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr19:58578313C>T	ENST00000313434.5	+	5	562	c.461C>T	c.(460-462)aCg>aTg	p.T154M	ZNF135_ENST00000401053.4_Missense_Mutation_p.T178M|ZNF135_ENST00000511556.1_Missense_Mutation_p.T166M|ZNF135_ENST00000506786.1_Missense_Mutation_p.T112M|ZNF135_ENST00000359978.6_Missense_Mutation_p.T166M|ZNF135_ENST00000439855.2_Missense_Mutation_p.T154M	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	154					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T178K(1)|p.T154K(1)		breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		CCTGTGAAGACGCCTGTTCTG	0.557																																						uc010yhq.1																			2	Substitution - Missense(2)		lung(2)	ovary(1)	1						c.(496-498)ACG>ATG		zinc finger protein 135 isoform 2							76.0	65.0	69.0					19																	58578313		2203	4300	6503	SO:0001583	missense	7694				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding	g.chr19:58578313C>T	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"""Zinc fingers, C2H2-type"", ""-"""	12919	protein-coding gene	gene with protein product		604077	"""zinc finger protein 61"", ""zinc finger protein 135 (clone pHZ-17)"""	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.461C>T	19.37:g.58578313C>T	ENSP00000321406:p.Thr154Met					ZNF135_uc002qre.2_Missense_Mutation_p.T154M|ZNF135_uc002qrd.1_Missense_Mutation_p.T112M|ZNF135_uc002qrf.2_Missense_Mutation_p.T112M|ZNF135_uc002qrg.2_Missense_Mutation_p.T124M|ZNF135_uc010yhr.1_Translation_Start_Site	p.T166M	NM_003436	NP_003427	B4DHH9	B4DHH9_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)	5	593	+		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)	166					B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	37	c.497C>T		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.76|12.76	2.033632|2.033632	0.35893|0.35893	.|.	.|.	ENSG00000176293|ENSG00000176293	ENST00000391699|ENST00000504540;ENST00000401053;ENST00000359978;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	.|T;T;T;T;T;T	.|0.06449	.|3.38;3.48;3.42;3.42;3.4;3.3	3.48|3.48	-3.58|-3.58	0.04597|0.04597	.|.	.|.	.|.	.|.	.|.	T|T	0.04048|0.04048	0.0113|0.0113	L|L	0.39898|0.39898	1.24|1.24	0.09310|0.09310	N|N	1|1	.|P;P;P	.|0.50443	.|0.935;0.935;0.935	.|B;B;B	.|0.38842	.|0.211;0.211;0.283	T|T	0.33879|0.33879	-0.9851|-0.9851	5|9	.|0.40728	.|T	.|0.16	.|.	3.2158|3.2158	0.06699|0.06699	0.4149:0.2279:0.0:0.3572|0.4149:0.2279:0.0:0.3572	.|.	.|166;154;166	.|E9PEV2;P52742;Q8N1I7	.|.;ZN135_HUMAN;.	C|M	172|166;178;166;154;154;166;112	.|ENSP00000441410:T178M;ENSP00000369437:T166M;ENSP00000444828:T154M;ENSP00000321406:T154M;ENSP00000422074:T166M;ENSP00000427691:T112M	.|ENSP00000321406:T154M	R|T	+|+	1|2	0|0	ZNF135|ZNF135	63270125|63270125	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.008000|0.008000	0.06430|0.06430	-0.422000|-0.422000	0.07043|0.07043	-0.348000|-0.348000	0.08286|0.08286	-0.321000|-0.321000	0.08615|0.08615	CGC|ACG		0.557	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436	
GALNT14	79623	broad.mit.edu	37	2	31360949	31360949	+	Missense_Mutation	SNP	G	G	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr2:31360949G>A	ENST00000349752.5	-	1	643	c.4C>T	c.(4-6)Cgg>Tgg	p.R2W	GALNT14_ENST00000420311.2_5'Flank|GALNT14_ENST00000324589.5_Missense_Mutation_p.R2W|GALNT14_ENST00000356174.3_Missense_Mutation_p.R2W	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14	2					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					GTCAGGCGCCGCATGGTCCCC	0.682																																						uc002rnr.2																			0				upper_aerodigestive_tract(2)|skin(1)	3						c.(4-6)CGG>TGG		N-acetylgalactosaminyltransferase 14							67.0	69.0	69.0					2																	31360949		2203	4300	6503	SO:0001583	missense	79623					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding	g.chr2:31360949G>A	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	22946	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 14"""	608225	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"""			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.4C>T	2.37:g.31360949G>A	ENSP00000288988:p.Arg2Trp					GALNT14_uc002rns.2_Missense_Mutation_p.R2W|GALNT14_uc010ymr.1_5'UTR|GALNT14_uc010ezo.1_Missense_Mutation_p.R2W|GALNT14_uc010ezp.1_Intron	p.R2W	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN			1	623	-	Acute lymphoblastic leukemia(172;0.155)		2			Cytoplasmic (Potential).		B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	37	c.4C>T	CCDS1773.2	.	.	.	.	.	.	.	.	.	.	G	19.04	3.749351	0.69533	.	.	ENSG00000158089	ENST00000349752;ENST00000324589;ENST00000356174;ENST00000430167	T;T;T;T	0.66280	0.37;-0.06;0.06;-0.2	4.29	-0.385	0.12470	.	.	.	.	.	T	0.60932	0.2307	M	0.67397	2.05	0.80722	D	1	D;D;D	0.64830	0.986;0.994;0.975	B;P;B	0.47744	0.432;0.556;0.249	T	0.62826	-0.6772	9	0.87932	D	0	.	8.1462	0.31113	0.0:0.1297:0.3668:0.5035	.	2;2;2	Q96FL9-2;Q96FL9-3;Q96FL9	.;.;GLT14_HUMAN	W	2	ENSP00000288988:R2W;ENSP00000314500:R2W;ENSP00000348497:R2W;ENSP00000406399:R2W	ENSP00000314500:R2W	R	-	1	2	GALNT14	31214453	1.000000	0.71417	0.998000	0.56505	0.931000	0.56810	0.957000	0.29215	0.005000	0.14708	0.313000	0.20887	CGG		0.682	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572	
ZAK	51776	broad.mit.edu	37	2	174104210	174104210	+	Missense_Mutation	SNP	G	G	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr2:174104210G>A	ENST00000375213.3	+	16	1423	c.1345G>A	c.(1345-1347)Gga>Aga	p.G449R	MLK7-AS1_ENST00000422703.1_RNA|MLTK_ENST00000409176.2_Missense_Mutation_p.G449R|MLK7-AS1_ENST00000423106.2_RNA	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		449					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										CTTGAAACCAGGAACTGGCCC	0.398																																						uc002uhz.2																			0				lung(3)|stomach(1)|ovary(1)|skin(1)	6						c.(1345-1347)GGA>AGA		MLK-related kinase isoform 1							58.0	59.0	58.0					2																	174104210		1813	4068	5881	SO:0001583	missense	51776				activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding	g.chr2:174104210G>A																												ENST00000375213.3:c.1345G>A	2.37:g.174104210G>A	ENSP00000364361:p.Gly449Arg					uc002uib.2_Intron	p.G449R	NM_016653	NP_057737	Q9NYL2	MLTK_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.176)		16	1545	+			449					B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	37	c.1345G>A	CCDS42777.1	.	.	.	.	.	.	.	.	.	.	G	19.84	3.901821	0.72754	.	.	ENSG00000091436	ENST00000409176;ENST00000375213	T;T	0.79141	-1.24;-1.24	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.81711	0.4880	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	P	0.60173	0.87	T	0.82242	-0.0554	10	0.52906	T	0.07	.	19.6483	0.95791	0.0:0.0:1.0:0.0	.	449	Q9NYL2	MLTK_HUMAN	R	449	ENSP00000387259:G449R;ENSP00000364361:G449R	ENSP00000364361:G449R	G	+	1	0	AC013461.1	173812456	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.017000	0.88712	2.697000	0.92050	0.643000	0.83706	GGA		0.398	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1		
SEMG2	6407	broad.mit.edu	37	20	43851147	43851147	+	Missense_Mutation	SNP	C	C	T	rs140069155	byFrequency	TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr20:43851147C>T	ENST00000372769.3	+	2	964	c.874C>T	c.(874-876)Cgt>Tgt	p.R292C		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	292	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)	p.R292S(1)		autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				CCCGTCTTCACGTACAGAAGA	0.393													C|||	3	0.000599042	0.0	0.0	5008	,	,		23488	0.001		0.002	False		,,,				2504	0.0					uc010ggz.2																			1	Substitution - Missense(1)		lung(1)	skin(1)	1						c.(874-876)CGT>TGT		semenogelin II precursor		C	CYS/ARG	0,4406		0,0,2203	94.0	88.0	90.0		874	-1.7	0.0	20	dbSNP_134	90	5,8595	4.3+/-15.6	0,5,4295	yes	missense	SEMG2	NM_003008.2	180	0,5,6498	TT,TC,CC		0.0581,0.0,0.0384	possibly-damaging	292/583	43851147	5,13001	2203	4300	6503	SO:0001583	missense	6407				sexual reproduction	extracellular space|stored secretory granule	structural molecule activity	g.chr20:43851147C>T		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"""Semenogelin 2"""	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.874C>T	20.37:g.43851147C>T	ENSP00000361855:p.Arg292Cys					SEMG2_uc002xnk.2_Missense_Mutation_p.R292C|SEMG2_uc002xnl.2_Missense_Mutation_p.R292C	p.R292C	NM_003008	NP_002999	Q02383	SEMG2_HUMAN			2	931	+		Myeloproliferative disorder(115;0.0122)	292			Repeat-rich region.|4 X 60 AA tandem repeats, type I.		Q53ZU2|Q6X2M5|Q6X2M6	Missense_Mutation	SNP	ENST00000372769.3	37	c.874C>T	CCDS13346.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	11.34	1.610816	0.28712	0.0	5.81E-4	ENSG00000124157	ENST00000372769	T	0.06449	3.3	1.28	-1.66	0.08265	.	.	.	.	.	T	0.07098	0.0180	N	0.14661	0.345	0.09310	N	1	D;D;D	0.67145	0.992;0.996;0.996	P;P;P	0.57283	0.817;0.806;0.806	T	0.32561	-0.9902	9	0.72032	D	0.01	.	5.7337	0.18055	0.4022:0.5978:0.0:0.0	.	292;292;292	A8K6Z6;Q6IRW3;Q02383	.;.;SEMG2_HUMAN	C	292	ENSP00000361855:R292C	ENSP00000361855:R292C	R	+	1	0	SEMG2	43284561	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.512000	0.00446	-0.525000	0.06391	-0.335000	0.08231	CGT		0.393	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008	
LMCD1	29995	broad.mit.edu	37	3	8574487	8574487	+	Missense_Mutation	SNP	C	C	T	rs199520704		TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr3:8574487C>T	ENST00000157600.3	+	2	339	c.107C>T	c.(106-108)tCg>tTg	p.S36L	LMCD1_ENST00000397386.3_Silent_p.F9F|LMCD1_ENST00000454244.1_Intron|LMCD1_ENST00000535732.1_Missense_Mutation_p.S36L|LMCD1-AS1_ENST00000439407.1_RNA	NM_014583.2	NP_055398.1	Q9NZU5	LMCD1_HUMAN	LIM and cysteine-rich domains 1	36	Cys-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|regulation of cardiac muscle hypertrophy (GO:0010611)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)	16				OV - Ovarian serous cystadenocarcinoma(96;0.124)		GGGACGTGTTCGGGCTTCGAG	0.537													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16681	0.0		0.0	False		,,,				2504	0.0					uc003bqq.2																			0				ovary(1)	1						c.(106-108)TCG>TTG		LIM and cysteine-rich domains 1							156.0	151.0	153.0					3																	8574487		2203	4300	6503	SO:0001583	missense	29995				positive regulation of calcineurin-NFAT signaling pathway|regulation of cardiac muscle hypertrophy|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus	transcription corepressor activity|zinc ion binding	g.chr3:8574487C>T	AF169284	CCDS33688.1, CCDS63533.1, CCDS63534.1	3p26-p24	2008-07-18			ENSG00000071282	ENSG00000071282			6633	protein-coding gene	gene with protein product	"""dyxin"""	604859				10662546	Standard	NM_001278233		Approved		uc003bqq.4	Q9NZU5	OTTHUMG00000154971	ENST00000157600.3:c.107C>T	3.37:g.8574487C>T	ENSP00000157600:p.Ser36Leu					LMCD1_uc011atd.1_Intron|LMCD1_uc011ate.1_Silent_p.F9F	p.S36L	NM_014583	NP_055398	Q9NZU5	LMCD1_HUMAN		OV - Ovarian serous cystadenocarcinoma(96;0.124)	2	221	+			36			Cys-rich.		B4DG80	Missense_Mutation	SNP	ENST00000157600.3	37	c.107C>T	CCDS33688.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	14.16	2.452342	0.43531	.	.	ENSG00000071282	ENST00000157600;ENST00000415597;ENST00000535732	T;T;T	0.29397	1.57;1.57;1.57	5.39	4.51	0.55191	.	0.468733	0.19668	N	0.108823	T	0.26484	0.0647	L	0.52573	1.65	0.80722	D	1	B	0.27656	0.184	B	0.19391	0.025	T	0.04509	-1.0946	10	0.39692	T	0.17	-10.0403	9.7711	0.40589	0.0:0.8327:0.0:0.1673	.	36	Q9NZU5	LMCD1_HUMAN	L	36;42;36	ENSP00000157600:S36L;ENSP00000400555:S42L;ENSP00000441100:S36L	ENSP00000157600:S36L	S	+	2	0	LMCD1	8549487	0.487000	0.25988	0.339000	0.25562	0.721000	0.41392	1.641000	0.37197	1.276000	0.44395	0.467000	0.42956	TCG		0.537	LMCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337854.1	NM_014583	
TLR9	54106	broad.mit.edu	37	3	52257538	52257538	+	Missense_Mutation	SNP	C	C	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr3:52257538C>A	ENST00000360658.2	-	2	1427	c.794G>T	c.(793-795)tGc>tTc	p.C265F	TLR9_ENST00000494383.1_Silent_p.L418L|TLR9_ENST00000597542.1_Missense_Mutation_p.C289F	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	265					defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	GCACTCCATGCAGGGGTTGGG	0.617																																						uc003dda.1																			0				large_intestine(2)|skin(2)	4						c.(793-795)TGC>TTC		toll-like receptor 9 isoform A precursor	Chloroquine(DB00608)						44.0	38.0	40.0					3																	52257538		2203	4300	6503	SO:0001583	missense	54106				defense response to bacterium|fibroblast growth factor receptor signaling pathway|I-kappaB phosphorylation|inflammatory response|innate immune response|insulin receptor signaling pathway|maintenance of gastrointestinal epithelium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-beta production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|response to molecule of bacterial origin	apical plasma membrane|basolateral plasma membrane|early phagosome|endoplasmic reticulum membrane|endosome membrane|extracellular region|integral to membrane|lysosome	interleukin-1 receptor binding|siRNA binding|transmembrane receptor activity	g.chr3:52257538C>A	AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"""CD molecules"""	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.794G>T	3.37:g.52257538C>A	ENSP00000353874:p.Cys265Phe					TLR9_uc003ddb.2_Missense_Mutation_p.C362F	p.C265F	NM_017442	NP_059138	Q9NR96	TLR9_HUMAN		BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	2	1428	-			265			LRR 8.|Extracellular (Potential).		B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	37	c.794G>T	CCDS2848.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.504772	0.85176	.	.	ENSG00000239732	ENST00000360658	T	0.28255	1.62	5.38	5.38	0.77491	.	0.000000	0.39687	N	0.001290	T	0.61198	0.2328	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.998	T	0.67405	-0.5679	10	0.87932	D	0	.	16.6158	0.84915	0.0:1.0:0.0:0.0	.	362;265	B4E0A1;Q9NR96	.;TLR9_HUMAN	F	265	ENSP00000353874:C265F	ENSP00000353874:C265F	C	-	2	0	TLR9	52232578	1.000000	0.71417	0.949000	0.38748	0.857000	0.48899	4.615000	0.61190	2.521000	0.84997	0.655000	0.94253	TGC		0.617	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1		
U2SURP	23350	broad.mit.edu	37	3	142773820	142773820	+	Missense_Mutation	SNP	G	G	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr3:142773820G>A	ENST00000473835.2	+	27	2900	c.2810G>A	c.(2809-2811)cGc>cAc	p.R937H	U2SURP_ENST00000493598.2_Missense_Mutation_p.R936H|U2SURP_ENST00000397933.2_Missense_Mutation_p.R528H	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	937	Arg/Ser-rich.				RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						AGCCCATCTCGCAGTAGCAGT	0.478																																						uc003evh.1																			0					0						c.(2809-2811)CGC>CAC		U2-associated SR140 protein							62.0	58.0	59.0					3																	142773820		1928	4140	6068	SO:0001583	missense	23350				RNA processing	nucleus	nucleotide binding|RNA binding	g.chr3:142773820G>A	BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"""RNA binding motif (RRM) containing"""	30855	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein a"", ""Ser/Arg-rich domain protein, 140 kDa"", ""U2 associated SR140 protein"""					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.2810G>A	3.37:g.142773820G>A	ENSP00000418563:p.Arg937His					SR140_uc003evi.1_Missense_Mutation_p.R528H|SR140_uc003evj.1_RNA|SR140_uc003evk.1_Missense_Mutation_p.R936H	p.R937H	NM_001080415	NP_001073884	O15042	SR140_HUMAN			27	2909	+			937			Arg/Ser-rich.		A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Missense_Mutation	SNP	ENST00000473835.2	37	c.2810G>A	CCDS46928.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.430878	0.83776	.	.	ENSG00000163714	ENST00000473835;ENST00000319822;ENST00000397933;ENST00000493598	T;T;T	0.46451	0.87;0.87;0.87	5.74	5.74	0.90152	.	0.097443	0.64402	D	0.000001	T	0.43411	0.1246	L	0.40543	1.245	0.80722	D	1	P;D;P	0.57257	0.948;0.979;0.913	B;P;B	0.45474	0.361;0.482;0.198	T	0.23655	-1.0182	10	0.44086	T	0.13	-4.6453	20.2982	0.98569	0.0:0.0:1.0:0.0	.	936;528;937	O15042-2;O15042-3;O15042	.;.;SR140_HUMAN	H	937;937;528;936	ENSP00000418563:R937H;ENSP00000381027:R528H;ENSP00000422011:R936H	ENSP00000322376:R937H	R	+	2	0	U2SURP	144256510	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.184000	0.94893	2.873000	0.98535	0.563000	0.77884	CGC		0.478	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415	
PIK3CA	5290	broad.mit.edu	37	3	178921548	178921548	+	Missense_Mutation	SNP	G	G	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr3:178921548G>A	ENST00000263967.3	+	5	1187	c.1030G>A	c.(1030-1032)Gtg>Atg	p.V344M		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	344	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				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.V344M(6)		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)	TGCAACCTACGTGAATGTAAA	0.308		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	uc003fjk.2		57		Dom	yes		3	3q26.3	5290	Mis	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			"""E, O"""			colorectal|gastric|gliobastoma|breast		6	Substitution - Missense(6)	p.V344A(1)|p.V344G(1)	endometrium(4)|ovary(2)	breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553						c.(1030-1032)GTG>ATG		phosphoinositide-3-kinase, catalytic, alpha							68.0	68.0	68.0					3																	178921548		1809	4073	5882	SO:0001583	missense	5290				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	g.chr3:178921548G>A		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.1030G>A	3.37:g.178921548G>A	ENSP00000263967:p.Val344Met	HNSCC(19;0.045)|TSP Lung(28;0.18)					p.V344M	NM_006218	NP_006209	P42336	PK3CA_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		5	1187	+	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		344					Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	c.1030G>A	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.709120	0.89018	.	.	ENSG00000121879	ENST00000263967	T	0.71103	-0.54	5.41	5.41	0.78517	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (1);	0.000000	0.85682	D	0.000000	D	0.82765	0.5108	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.66196	0.942	T	0.83027	-0.0164	10	0.54805	T	0.06	-22.945	19.5423	0.95278	0.0:0.0:1.0:0.0	.	344	P42336	PK3CA_HUMAN	M	344	ENSP00000263967:V344M	ENSP00000263967:V344M	V	+	1	0	PIK3CA	180404242	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.358000	0.97109	2.682000	0.91365	0.491000	0.48974	GTG		0.308	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
PIK3R1	5295	broad.mit.edu	37	5	67591152	67591152	+	Splice_Site	DEL	T	T	-			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr5:67591152delT	ENST00000521381.1	+	13	2361	c.1745delT	c.(1744-1746)atg>ag	p.M582fs	PIK3R1_ENST00000521657.1_Splice_Site_p.M582fs|PIK3R1_ENST00000396611.1_Splice_Site_p.M582fs|PIK3R1_ENST00000523872.1_Splice_Site_p.M219fs|PIK3R1_ENST00000336483.5_Splice_Site_p.M312fs|PIK3R1_ENST00000274335.5_Splice_Site_p.M582fs|PIK3R1_ENST00000320694.8_Splice_Site_p.M282fs	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	582					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|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)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|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 cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.R577_M582>K(1)|p.Y580fs*1(1)|p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	CAATACTTGATGTAAGTATTT	0.373			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																												uc003jva.2				Rec	yes		5	5q13.1	5295	Mis|F|O	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""			"""E, O"""			gliobastoma|ovarian|colorectal		4	Whole gene deletion(1)|Complex - deletion inframe(1)|Deletion - Frameshift(1)|Unknown(1)	p.M582_D605>I(4)|p.R577_M582>K(1)|p.Y580fs*1(1)|p.?(1)	large_intestine(1)|lung(1)|central_nervous_system(1)|endometrium(1)	endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101						c.(1744-1746)ATGfs		phosphoinositide-3-kinase, regulatory subunit 1	Isoproterenol(DB01064)						135.0	134.0	135.0					5																	67591152		2203	4300	6503	SO:0001630	splice_region_variant	5295				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	g.chr5:67591152delT	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1745+1T>-	5.37:g.67591152delT		TCGA GBM(4;<1E-08)				PIK3R1_uc003jvb.2_Frame_Shift_Del_p.M582fs|PIK3R1_uc003jvc.2_Frame_Shift_Del_p.M282fs|PIK3R1_uc003jvd.2_Frame_Shift_Del_p.M312fs|PIK3R1_uc003jve.2_Frame_Shift_Del_p.M261fs|PIK3R1_uc011crb.1_Frame_Shift_Del_p.M252fs	p.M582fs	NM_181523	NP_852664	P27986	P85A_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	13	2305	+		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)	582					B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Frame_Shift_Del	DEL	ENST00000521381.1	37	c.1745delT	CCDS3993.1																																																																																				0.373	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	Frame_Shift_Del
AFF4	27125	broad.mit.edu	37	5	132227876	132227877	+	Frame_Shift_Ins	INS	-	-	G			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr5:132227876_132227877insG	ENST00000265343.5	-	13	2995_2996	c.2616_2617insC	c.(2614-2619)tccagtfs	p.S873fs	AFF4_ENST00000378595.3_Frame_Shift_Ins_p.S873fs	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	873	Ser-rich.				spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTGGAGCTACTGGAAGTCTTCC	0.47																																					Ovarian(126;889 1733 2942 10745 11605)	uc003kyd.2																			0				ovary(2)|kidney(2)|skin(1)	5						c.(2614-2619)TCCAGTfs		ALL1 fused gene from 5q31																																				SO:0001589	frameshift_variant	27125				transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity	g.chr5:132227876_132227877insG	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"""ALL1 fused gene from 5q31"""	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.2617dupC	5.37:g.132227878_132227878dupG	ENSP00000265343:p.Ser873fs					AFF4_uc011cxk.1_Frame_Shift_Ins_p.S550fs|AFF4_uc003kye.1_Frame_Shift_Ins_p.S872fs	p.S872fs	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		13	3024_3025	-		all_cancers(142;0.145)|Breast(839;0.198)	872_873			Ser-rich.		B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Frame_Shift_Ins	INS	ENST00000265343.5	37	c.2616_2617insC	CCDS4164.1																																																																																				0.470	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423	
PCDHA6	56142	broad.mit.edu	37	5	140209539	140209539	+	Silent	SNP	G	G	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr5:140209539G>A	ENST00000529310.1	+	1	1977	c.1863G>A	c.(1861-1863)ccG>ccA	p.P621P	PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	621	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCGCTTCCCGTTTCGCGTGG	0.657																																						uc003lho.2																			0				haematopoietic_and_lymphoid_tissue(1)|skin(1)	2						c.(1861-1863)CCG>CCA		protocadherin alpha 6 isoform 1 precursor							72.0	76.0	75.0					5																	140209539		2203	4300	6503	SO:0001819	synonymous_variant	56142				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding	g.chr5:140209539G>A	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"""Cadherins / Protocadherins : Clustered"""	8672	other	complex locus constituent	"""KIAA0345-like 8"""	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1863G>A	5.37:g.140209539G>A						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc011dab.1_Silent_p.P621P	p.P621P	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	1890	+			621			Cadherin 6.|Extracellular (Potential).		O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	37	c.1863G>A	CCDS47281.1																																																																																				0.657	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909	
SH3RF2	153769	broad.mit.edu	37	5	145439569	145439569	+	Missense_Mutation	SNP	G	G	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr5:145439569G>A	ENST00000511217.1	+	8	1748	c.1696G>A	c.(1696-1698)Gtg>Atg	p.V566M	SH3RF2_ENST00000511705.1_3'UTR|SH3RF2_ENST00000359120.4_Missense_Mutation_p.V566M			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	566					negative regulation of phosphatase activity (GO:0010923)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCCCTCAGCCGTGGTGGTGGA	0.672																																						uc003lnt.2																			0				ovary(1)|skin(1)	2						c.(1696-1698)GTG>ATG		SH3 domain containing ring finger 2							62.0	58.0	60.0					5																	145439569		2203	4300	6503	SO:0001583	missense	153769						ligase activity|protein phosphatase 1 binding|zinc ion binding	g.chr5:145439569G>A	AL833297	CCDS4280.1	5q32	2013-01-09	2011-11-04	2011-11-04	ENSG00000156463	ENSG00000156463		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26299	protein-coding gene	gene with protein product	"""heart protein phosphatase 1-binding protein"", ""POSH-eliminating RING protein"""	613377	"""protein phosphatase 1, regulatory subunit 39"""	PPP1R39		22128169	Standard	NM_152550		Approved	FLJ23654, RNF158, Hepp1, POSHER	uc003lnt.3	Q8TEC5	OTTHUMG00000129685	ENST00000511217.1:c.1696G>A	5.37:g.145439569G>A	ENSP00000424497:p.Val566Met					SH3RF2_uc011dbl.1_Missense_Mutation_p.V566M|SH3RF2_uc011dbm.1_Missense_Mutation_p.V51M|SH3RF2_uc003lnu.2_Missense_Mutation_p.V57M|SH3RF2_uc011dbn.1_Missense_Mutation_p.V57M|SH3RF2_uc011dbo.1_Missense_Mutation_p.V23M	p.V566M	NM_152550	NP_689763	Q8TEC5	SH3R2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		9	1934	+			566					A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Missense_Mutation	SNP	ENST00000511217.1	37	c.1696G>A	CCDS4280.1	.	.	.	.	.	.	.	.	.	.	A	1.061	-0.672990	0.03403	.	.	ENSG00000156463	ENST00000359120;ENST00000511217	T;T	0.18960	2.18;2.18	5.09	-2.49	0.06403	.	1.488470	0.03973	N	0.292065	T	0.13457	0.0326	N	0.22421	0.69	0.09310	N	1	B;B	0.20671	0.013;0.047	B;B	0.11329	0.006;0.005	T	0.28235	-1.0050	10	0.32370	T	0.25	0.3123	6.7443	0.23453	0.4162:0.0:0.4735:0.1103	.	57;566	Q8TEC5-2;Q8TEC5	.;SH3R2_HUMAN	M	566	ENSP00000352028:V566M;ENSP00000424497:V566M	ENSP00000352028:V566M	V	+	1	0	SH3RF2	145419762	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.007000	0.12810	-0.465000	0.06953	-1.430000	0.01095	GTG		0.672	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1	NM_152550	
RIMS1	22999	broad.mit.edu	37	6	72957754	72957754	+	Missense_Mutation	SNP	C	C	A			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr6:72957754C>A	ENST00000521978.1	+	12	2165	c.2165C>A	c.(2164-2166)cCt>cAt	p.P722H	RIMS1_ENST00000520567.1_Missense_Mutation_p.P722H|RIMS1_ENST00000523963.1_Missense_Mutation_p.P196H|RIMS1_ENST00000425662.2_Missense_Mutation_p.P115H|RIMS1_ENST00000348717.5_Missense_Mutation_p.P722H|RIMS1_ENST00000517960.1_Missense_Mutation_p.P722H|RIMS1_ENST00000522291.1_Missense_Mutation_p.P722H|RIMS1_ENST00000264839.7_Missense_Mutation_p.P722H|RIMS1_ENST00000517827.1_Missense_Mutation_p.P181H|RIMS1_ENST00000401910.3_Missense_Mutation_p.P196H|RIMS1_ENST00000491071.2_Missense_Mutation_p.P722H|RIMS1_ENST00000518273.1_Missense_Mutation_p.P722H	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	722					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				ATGGAAAGGCCTTCCATTTCT	0.333																																						uc003pga.2																			0				ovary(7)|pancreas(2)|breast(1)	10						c.(2164-2166)CCT>CAT		regulating synaptic membrane exocytosis 1							130.0	122.0	124.0					6																	72957754		1813	4073	5886	SO:0001583	missense	22999				calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding	g.chr6:72957754C>A	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2165C>A	6.37:g.72957754C>A	ENSP00000428417:p.Pro722His					RIMS1_uc011dyb.1_Missense_Mutation_p.P348H|RIMS1_uc003pgc.2_Missense_Mutation_p.P348H|RIMS1_uc010kaq.2_Missense_Mutation_p.P196H|RIMS1_uc011dyc.1_Missense_Mutation_p.P196H|RIMS1_uc010kar.2_Missense_Mutation_p.P115H|RIMS1_uc011dyd.1_Missense_Mutation_p.P181H|RIMS1_uc003pgf.2_5'Flank|RIMS1_uc003pgg.2_5'Flank|RIMS1_uc003pgi.2_5'Flank|RIMS1_uc003pgh.2_5'Flank|RIMS1_uc003pgd.2_5'Flank|RIMS1_uc003pge.2_5'Flank|RIMS1_uc003pgb.3_Missense_Mutation_p.P348H|RIMS1_uc010kas.1_Missense_Mutation_p.P181H	p.P722H	NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN			12	2242	+		all_epithelial(107;0.179)|all_hematologic(105;0.212)	722					A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	c.2165C>A	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.981824	0.93044	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827	T;T;T;T;T;T;T;T;T;T;T;T;T	0.20069	2.1;2.26;2.17;2.26;2.25;2.24;2.26;2.15;2.26;2.22;2.27;2.19;2.25	5.68	5.68	0.88126	.	0.000000	0.64402	D	0.000003	T	0.31358	0.0794	L	0.34521	1.04	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.85130	0.984;0.997;0.997;0.979;0.993;0.997;0.962	T	0.05733	-1.0867	10	0.87932	D	0	-15.1679	20.1615	0.98135	0.0:1.0:0.0:0.0	.	181;196;722;181;196;722;722	B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;C9JNW6;Q86UR5	.;.;.;.;.;.;RIMS1_HUMAN	H	722;722;722;722;722;722;722;722;722;722;722;722;196;196;115;115;181	ENSP00000430101:P722H;ENSP00000275037:P722H;ENSP00000264839:P722H;ENSP00000429959:P722H;ENSP00000430408:P722H;ENSP00000430502:P722H;ENSP00000430932:P722H;ENSP00000428417:P722H;ENSP00000385649:P196H;ENSP00000428328:P196H;ENSP00000411235:P115H;ENSP00000389503:P115H;ENSP00000428367:P181H	ENSP00000264839:P722H	P	+	2	0	RIMS1	73014475	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.835000	0.97688	0.650000	0.86243	CCT		0.333	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
DENND2A	27147	broad.mit.edu	37	7	140301861	140301861	+	Missense_Mutation	SNP	C	C	T			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr7:140301861C>T	ENST00000275884.6	-	2	754	c.337G>A	c.(337-339)Gga>Aga	p.G113R	DENND2A_ENST00000496613.1_Missense_Mutation_p.G113R|DENND2A_ENST00000537639.1_Missense_Mutation_p.G113R|DENND2A_ENST00000492720.1_Missense_Mutation_p.G113R			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	113					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					TTCACTGCTCCTTTATTCCTC	0.587																																						uc010lnj.2																			0				ovary(3)|breast(1)	4						c.(337-339)GGA>AGA		DENN/MADD domain containing 2A							178.0	180.0	179.0					7																	140301861		2068	4209	6277	SO:0001583	missense	27147							g.chr7:140301861C>T	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"""DENN/MADD domain containing"""	22212	protein-coding gene	gene with protein product			"""KIAA1277"""	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.337G>A	7.37:g.140301861C>T	ENSP00000275884:p.Gly113Arg					DENND2A_uc011kre.1_RNA|DENND2A_uc010lnk.2_Missense_Mutation_p.G113R|DENND2A_uc003vvw.2_Missense_Mutation_p.G113R|DENND2A_uc003vvx.2_Missense_Mutation_p.G113R	p.G113R	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN			1	482	-	Melanoma(164;0.00956)		113					C9JUI3|Q1RMD5|Q86XY0	Missense_Mutation	SNP	ENST00000275884.6	37	c.337G>A	CCDS43659.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.601362	0.28534	.	.	ENSG00000146966	ENST00000275884;ENST00000537639;ENST00000496613;ENST00000492720;ENST00000491728	T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22	5.13	2.33	0.28932	.	1.407880	0.04144	N	0.320113	T	0.60340	0.2261	N	0.08118	0	0.09310	N	1	P;B	0.41524	0.753;0.012	B;B	0.37304	0.246;0.027	T	0.55976	-0.8055	10	0.62326	D	0.03	-1.909	6.3411	0.21322	0.0:0.64:0.1329:0.2271	.	113;113	Q9ULE3-2;Q9ULE3	.;DEN2A_HUMAN	R	113	ENSP00000275884:G113R;ENSP00000442245:G113R;ENSP00000419654:G113R;ENSP00000419464:G113R;ENSP00000418844:G113R	ENSP00000275884:G113R	G	-	1	0	DENND2A	139948330	0.003000	0.15002	0.000000	0.03702	0.004000	0.04260	1.619000	0.36965	0.318000	0.23185	0.655000	0.94253	GGA		0.587	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689	
OR13C5	138799	broad.mit.edu	37	9	107361451	107361452	+	Frame_Shift_Del	DEL	GC	GC	-	rs376107801|rs201540433|rs377523807|rs199665292	byFrequency	TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chr9:107361451_107361452delGC	ENST00000374779.2	-	1	336_337	c.243_244delGC	c.(241-246)acgctafs	p.L82fs		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AAGCTCACTAGCGTGGAGGGAA	0.51																																						uc011lvp.1																			0				ovary(2)|pancreas(1)|skin(1)	4						c.(241-246)ACGCTAfs		olfactory receptor, family 13, subfamily C,																																				SO:0001589	frameshift_variant	138799				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr9:107361451_107361452delGC		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.243_244delGC	9.37:g.107361451_107361452delGC	ENSP00000363911:p.Leu82fs						p.T81fs	NM_001004482	NP_001004482	Q8NGS8	O13C5_HUMAN			1	243_244	-			81_82			Extracellular (Potential).		B2RNE5|B9EGW5|Q6IF53	Frame_Shift_Del	DEL	ENST00000374779.2	37	c.243_244delGC	CCDS35091.1																																																																																				0.510	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
CXorf66	347487	broad.mit.edu	37	X	139038184	139038184	+	Silent	SNP	T	T	C			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chrX:139038184T>C	ENST00000370540.1	-	3	980	c.957A>G	c.(955-957)gcA>gcG	p.A319A		NM_001013403.2	NP_001013421.1	Q5JRM2	CX066_HUMAN	chromosome X open reading frame 66	319						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|skin(1)|stomach(1)	26						GATCACCGTATGCATTGTTCC	0.383																																						uc004fbb.2																			0					0						c.(955-957)GCA>GCG		hypothetical protein LOC347487 precursor							220.0	184.0	196.0					X																	139038184		2203	4300	6503	SO:0001819	synonymous_variant	347487					integral to membrane		g.chrX:139038184T>C		CCDS35411.1	Xq27.1	2014-05-30			ENSG00000203933	ENSG00000203933			33743	protein-coding gene	gene with protein product	"""secreted glycoprotein, X-linked"""					24709545	Standard	NM_001013403		Approved	RP11-35F15.2, SGPX	uc004fbb.3	Q5JRM2	OTTHUMG00000022539	ENST00000370540.1:c.957A>G	X.37:g.139038184T>C							p.A319A	NM_001013403	NP_001013421	Q5JRM2	CX066_HUMAN			3	979	-			319			Cytoplasmic (Potential).			Silent	SNP	ENST00000370540.1	37	c.957A>G	CCDS35411.1																																																																																				0.383	CXorf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058572.1	NM_001013403	
UBE2NL	389898	broad.mit.edu	37	X	142967295	142967295	+	Silent	SNP	C	C	T			TCGA-19-5947-01A-11D-1696-08	TCGA-19-5947-11A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	d5e7dd90-ead0-40fe-94c5-bc740cb509ab	fa48fd89-0ab3-4670-9276-3257e1451d5d	g.chrX:142967295C>T	ENST00000370494.1	+	1	123	c.93C>T	c.(91-93)aaC>aaT	p.N31N		NM_001012989.1	NP_001013007.1	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like (gene/pseudogene)	31						extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)			breast(1)|endometrium(1)|large_intestine(8)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(192;6.56e-05)					ATGAAAGCAACGCCCGTTATT	0.493																																						uc004fca.2																			0					0						c.(91-93)AAC>AAT		ubiquitin-conjugating enzyme E2N-like							85.0	82.0	83.0					X																	142967295		2203	4300	6503	SO:0001819	synonymous_variant	389898						acid-amino acid ligase activity	g.chrX:142967295C>T			Xq27.3	2014-06-11	2014-06-11		ENSG00000102069			"""Ubiquitin-conjugating enzymes E2"""	31710	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2N-like"""			20736409	Standard	NM_001012989		Approved		uc004fca.3	Q5JXB2	OTTHUMG00000022586	ENST00000370494.1:c.93C>T	X.37:g.142967295C>T							p.N31N	NM_001012989	NP_001013007	Q5JXB2	UE2NL_HUMAN			1	123	+	Acute lymphoblastic leukemia(192;6.56e-05)		31					E9KL27	Silent	SNP	ENST00000370494.1	37	c.93C>T	CCDS35420.1																																																																																				0.493	UBE2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058624.1	NM_001012989	
