#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_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
IGHV4-34	28395	broad.mit.edu	37	14	106829621	106829621	+	RNA	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr14:106829621C>T	ENST00000390616.2	-	0	372									immunoglobulin heavy variable 4-34																		CAGCCGTGTCCGCGGCGGTCA	0.587																																						ENST00000390616.2																			0																				151.0	155.0	154.0					14																	106829621		1919	4119	6038			0							g.chr14:106829621C>T	X92278		14q32.33	2012-02-08			ENSG00000211956	ENSG00000211956		"""Immunoglobulins / IGH locus"""	5650	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152074		14.37:g.106829621C>T			Somatic								WXS	Illumina GAIIx	Phase_I					0	372	-									RNA	SNP	ENST00000390616.2	37																																																																																						0.587	IGHV4-34-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325168.1	NG_001019		5	175	0	0	0	1	0	5	175				
DENND3	22898	broad.mit.edu	37	8	142161751	142161751	+	Missense_Mutation	SNP	G	G	A	rs571831372		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr8:142161751G>A	ENST00000262585.2	+	7	927	c.649G>A	c.(649-651)Gtc>Atc	p.V217I	DENND3_ENST00000519811.1_Missense_Mutation_p.V297I|DENND3_ENST00000424248.1_Missense_Mutation_p.V217I	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	217	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			ACAGCGGATCGTCTTCTTCTC	0.542													G|||	1	0.000199681	0.0	0.0	5008	,	,		16882	0.0		0.001	False		,,,				2504	0.0					ENST00000519811.1																			0				breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55						c.(889-891)Gtc>Atc		DENN/MADD domain containing 3							150.0	121.0	131.0					8																	142161751		2203	4300	6503	SO:0001583	missense	22898							g.chr8:142161751G>A	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"""DENN/MADD domain containing"", ""WD repeat domain containing"""	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.649G>A	8.37:g.142161751G>A	ENSP00000262585:p.Val217Ile		Somatic				DENND3_ENST00000262585.2_Missense_Mutation_p.V217I|DENND3_ENST00000424248.1_Missense_Mutation_p.V217I	p.V297I			WXS	Illumina GAIIx	Phase_I	A2RUS2	DEND3_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.105)		7	959	+	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		217					B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	37	c.889G>A	CCDS34947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.52|19.52	3.842905|3.842905	0.71488|0.71488	.|.	.|.	ENSG00000105339|ENSG00000105339	ENST00000518668|ENST00000262585;ENST00000424248;ENST00000519811;ENST00000520986	.|T;T;T;T	.|0.07800	.|3.16;3.16;3.16;3.16	5.38|5.38	5.38|5.38	0.77491|0.77491	.|DENN (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.21801|0.21801	0.0525|0.0525	L|L	0.41573|0.41573	1.285|1.285	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.992	T|T	0.01679|0.01679	-1.1297|-1.1297	5|10	.|0.25106	.|T	.|0.35	-16.2549|-16.2549	19.1045|19.1045	0.93287|0.93287	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|297;217	.|E9PF32;A2RUS2	.|.;DEND3_HUMAN	H|I	273|217;217;297;219	.|ENSP00000262585:V217I;ENSP00000410594:V217I;ENSP00000428714:V297I;ENSP00000429780:V219I	.|ENSP00000262585:V217I	R|V	+|+	2|1	0|0	DENND3|DENND3	142230933|142230933	1.000000|1.000000	0.71417|0.71417	0.752000|0.752000	0.31206|0.31206	0.181000|0.181000	0.23173|0.23173	9.107000|9.107000	0.94261|0.94261	2.506000|2.506000	0.84524|0.84524	0.563000|0.563000	0.77884|0.77884	CGT|GTC		0.542	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		20	118	0	0	0	1	0	20	118				
PITPNM2	57605	broad.mit.edu	37	12	123481386	123481386	+	Missense_Mutation	SNP	G	G	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr12:123481386G>T	ENST00000542749.1	-	10	1607	c.1544C>A	c.(1543-1545)cCc>cAc	p.P515H	PITPNM2_ENST00000320201.4_Missense_Mutation_p.P515H|PITPNM2_ENST00000280562.5_Missense_Mutation_p.P515H|PITPNM2_ENST00000392428.1_Missense_Mutation_p.P236H			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	515					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		GGCCAGCAGGGGGAGGGCAGC	0.637																																						ENST00000280562.5																			0				NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39						c.(1543-1545)cCc>cAc		phosphatidylinositol transfer protein, membrane-associated 2							49.0	49.0	49.0					12																	123481386		2203	4300	6503	SO:0001583	missense	57605				metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding	g.chr12:123481386G>T	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.1544C>A	12.37:g.123481386G>T	ENSP00000437611:p.Pro515His		Somatic				PITPNM2_ENST00000320201.4_Missense_Mutation_p.P515H|PITPNM2_ENST00000392428.1_Missense_Mutation_p.P236H|PITPNM2_ENST00000542749.1_Missense_Mutation_p.P515H	p.P515H			WXS	Illumina GAIIx	Phase_I	Q9BZ72	PITM2_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)	11	1749	-	all_neural(191;0.101)|Medulloblastoma(191;0.163)		515					Q9P271	Missense_Mutation	SNP	ENST00000542749.1	37	c.1544C>A	CCDS9242.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.002812	0.74932	.	.	ENSG00000090975	ENST00000280562;ENST00000320201;ENST00000392428;ENST00000542749	T;T;T;T	0.19669	2.13;2.13;2.13;2.13	4.81	3.92	0.45320	.	0.000000	0.85682	D	0.000000	T	0.48589	0.1508	M	0.82193	2.58	0.53688	D	0.999975	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.55153	-0.8185	10	0.87932	D	0	-17.2931	13.0406	0.58897	0.0784:0.0:0.9216:0.0	.	515;515	Q9BZ72-2;Q9BZ72	.;PITM2_HUMAN	H	515;515;236;515	ENSP00000280562:P515H;ENSP00000322218:P515H;ENSP00000376223:P236H;ENSP00000437611:P515H	ENSP00000280562:P515H	P	-	2	0	PITPNM2	122047339	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	7.976000	0.88070	1.033000	0.39918	0.460000	0.39030	CCC		0.637	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		18	19	1	0	8.34094e-07	1	8.58626e-07	18	19				
C2orf16	84226	broad.mit.edu	37	2	27804437	27804437	+	Silent	SNP	T	T	A	rs201236336	byFrequency	TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr2:27804437T>A	ENST00000408964.2	+	1	5049	c.4998T>A	c.(4996-4998)tcT>tcA	p.S1666S	ZNF512_ENST00000379717.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000416005.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1666	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GCAGTTCCTCTGAGAGAAGAC	0.577																																						ENST00000408964.2																			0				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47						c.(4996-4998)tcT>tcA		chromosome 2 open reading frame 16							153.0	156.0	155.0					2																	27804437		1905	4118	6023	SO:0001819	synonymous_variant	84226							g.chr2:27804437T>A	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4998T>A	2.37:g.27804437T>A			Somatic					p.S1666S	NM_032266.3	NP_115642.3	WXS	Illumina GAIIx	Phase_I	Q68DN1	CB016_HUMAN			1	5049	+	Acute lymphoblastic leukemia(172;0.155)		1666			27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.		B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	c.4998T>A	CCDS42666.1																																																																																				0.577	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		19	103	0	0	0	1	0	19	103				
NCF2	4688	broad.mit.edu	37	1	183529380	183529380	+	Missense_Mutation	SNP	T	T	G			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr1:183529380T>G	ENST00000367535.3	-	14	1570	c.1319A>C	c.(1318-1320)aAg>aCg	p.K440T	NCF2_ENST00000367536.1_Missense_Mutation_p.K440T|NCF2_ENST00000469280.1_Intron|NCF2_ENST00000418089.1_Missense_Mutation_p.K359T|NCF2_ENST00000413720.1_Missense_Mutation_p.K395T	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	440					aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	TTCACTTTCCTTGGGTTCATC	0.438																																						ENST00000413720.1																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30						c.(1183-1185)aAg>aCg		neutrophil cytosolic factor 2							217.0	201.0	207.0					1																	183529380		2203	4300	6503	SO:0001583	missense	4688				cellular defense response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex|nucleolus	electron carrier activity|protein C-terminus binding	g.chr1:183529380T>G	BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701		"""Tetratricopeptide (TTC) repeat domain containing"""	7661	protein-coding gene	gene with protein product	"""NADPH oxidase activator 2"", ""chronic granulomatous disease, autosomal 2"""	608515	"""neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"""				Standard	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	P19878	OTTHUMG00000035329	ENST00000367535.3:c.1319A>C	1.37:g.183529380T>G	ENSP00000356505:p.Lys440Thr		Somatic				NCF2_ENST00000469280.1_Intron|NCF2_ENST00000367535.3_Missense_Mutation_p.K440T|NCF2_ENST00000418089.1_Missense_Mutation_p.K359T|NCF2_ENST00000367536.1_Missense_Mutation_p.K440T	p.K395T	NM_001190794.1	NP_001177723.1	WXS	Illumina GAIIx	Phase_I	P19878	NCF2_HUMAN			13	1458	-			440		R -> W (in dbSNP:rs13306575).	OPR.		B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Missense_Mutation	SNP	ENST00000367535.3	37	c.1184A>C	CCDS1356.1	.	.	.	.	.	.	.	.	.	.	T	12.39	1.922659	0.33908	.	.	ENSG00000116701	ENST00000367536;ENST00000392014;ENST00000413720;ENST00000418089;ENST00000367535	T;T;T;T	0.70749	-0.51;-0.16;-0.05;-0.51	5.18	2.71	0.32032	Src homology-3 domain (1);	0.788960	0.11865	N	0.522014	T	0.58481	0.2125	L	0.47716	1.5	0.09310	N	1	B;B;B	0.24823	0.001;0.112;0.036	B;B;B	0.26416	0.001;0.069;0.021	T	0.43376	-0.9395	10	0.14656	T	0.56	-16.6308	5.4961	0.16804	0.3006:0.0:0.1559:0.5435	.	359;395;440	E9PHJ2;E9PHX3;P19878	.;.;NCF2_HUMAN	T	440;512;395;359;440	ENSP00000356506:K440T;ENSP00000399294:K395T;ENSP00000407217:K359T;ENSP00000356505:K440T	ENSP00000356505:K440T	K	-	2	0	NCF2	181796003	0.001000	0.12720	0.002000	0.10522	0.919000	0.55068	0.822000	0.27352	0.241000	0.21283	0.533000	0.62120	AAG		0.438	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1	NM_000433		34	57	0	0	0	1	0	34	57				
POM121L9P	29774	broad.mit.edu	37	22	24659593	24659593	+	RNA	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr22:24659593C>T	ENST00000414583.2	+	0	3118					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		TCACTGACATCGAAGGCTGCC	0.632																																						ENST00000414583.2																			0																																																			0							g.chr22:24659593C>T	AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659593C>T			Somatic						NR_003714.1		WXS	Illumina GAIIx	Phase_I					0	3118	+									RNA	SNP	ENST00000414583.2	37																																																																																						0.632	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1	NM_014549		3	15	0	0	0	1	0	3	15				
LMO3	55885	broad.mit.edu	37	12	16753678	16753678	+	Silent	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr12:16753678C>T	ENST00000320122.6	-	2	639	c.117G>A	c.(115-117)aaG>aaA	p.K39K	LMO3_ENST00000541846.1_Silent_p.K39K|LMO3_ENST00000447609.1_Silent_p.K39K|LMO3_ENST00000354662.1_Silent_p.K39K|LMO3_ENST00000261169.6_Silent_p.K50K|LMO3_ENST00000534946.1_Silent_p.K39K|LMO3_ENST00000537568.1_5'UTR|LMO3_ENST00000540445.1_Silent_p.K39K|LMO3_ENST00000540848.1_Silent_p.K39K|LMO3_ENST00000441439.2_Silent_p.K39K|LMO3_ENST00000535535.1_Silent_p.K39K|LMO3_ENST00000541295.1_Silent_p.K57K|LMO3_ENST00000537304.1_Silent_p.K39K	NM_001243611.1	NP_001230540.1	Q8TAP4	LMO3_HUMAN	LIM domain only 3 (rhombotin-like 2)	39	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|skin(1)	5		Hepatocellular(102;0.244)				AGCAGGCACACTTCAGGCAGT	0.498																																						ENST00000320122.6																			0				endometrium(2)|large_intestine(2)|skin(1)	5						c.(115-117)aaG>aaA		LIM domain only 3 (rhombotin-like 2)							154.0	133.0	140.0					12																	16753678		2203	4300	6503	SO:0001819	synonymous_variant	55885				regulation of transcription, DNA-dependent|transcription, DNA-dependent		zinc ion binding	g.chr12:16753678C>T	BC026311	CCDS8678.1, CCDS58210.1, CCDS58211.1, CCDS58212.1	12p13	2004-05-19			ENSG00000048540	ENSG00000048540			6643	protein-coding gene	gene with protein product		180386		RBTNL2		11489251	Standard	NM_018640		Approved	Rhom-3, DAT1	uc010shy.2	Q8TAP4	OTTHUMG00000168837	ENST00000320122.6:c.117G>A	12.37:g.16753678C>T			Somatic				LMO3_ENST00000534946.1_Silent_p.K39K|LMO3_ENST00000354662.1_Silent_p.K39K|LMO3_ENST00000540445.1_Silent_p.K39K|LMO3_ENST00000261169.6_Silent_p.K50K|LMO3_ENST00000541295.1_Silent_p.K57K|LMO3_ENST00000441439.2_Silent_p.K39K|LMO3_ENST00000537568.1_5'UTR|LMO3_ENST00000540848.1_Silent_p.K39K|LMO3_ENST00000535535.1_Silent_p.K39K|LMO3_ENST00000537304.1_Silent_p.K39K|LMO3_ENST00000447609.1_Silent_p.K39K|LMO3_ENST00000541846.1_Silent_p.K39K	p.K39K	NM_001243611.1	NP_001230540.1	WXS	Illumina GAIIx	Phase_I	Q8TAP4	LMO3_HUMAN			2	639	-		Hepatocellular(102;0.244)	39			LIM zinc-binding 1.		B4DG90|B4DH35|Q58A66|Q58A67|Q8N974|Q9UDD5	Silent	SNP	ENST00000320122.6	37	c.117G>A	CCDS8678.1																																																																																				0.498	LMO3-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401279.1	NM_018640		31	35	0	0	0	1	0	31	35				
C2orf16	84226	broad.mit.edu	37	2	27804422	27804422	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr2:27804422C>A	ENST00000408964.2	+	1	5034	c.4983C>A	c.(4981-4983)agC>agA	p.S1661R	ZNF512_ENST00000379717.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000416005.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1661	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CAGAGAGAAGCCATCGCAGTT	0.582																																						ENST00000408964.2																			0				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47						c.(4981-4983)agC>agA		chromosome 2 open reading frame 16							159.0	161.0	161.0					2																	27804422		1904	4127	6031	SO:0001583	missense	84226							g.chr2:27804422C>A	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4983C>A	2.37:g.27804422C>A	ENSP00000386190:p.Ser1661Arg		Somatic					p.S1661R	NM_032266.3	NP_115642.3	WXS	Illumina GAIIx	Phase_I	Q68DN1	CB016_HUMAN			1	5034	+	Acute lymphoblastic leukemia(172;0.155)		1661			27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.		B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	c.4983C>A	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	C	7.587	0.669947	0.14776	.	.	ENSG00000221843	ENST00000408964	T	0.05513	3.43	3.1	-1.3	0.09259	.	.	.	.	.	T	0.05640	0.0148	L	0.47716	1.5	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38112	-0.9676	9	0.48119	T	0.1	.	3.7016	0.08384	0.3288:0.4636:0.0:0.2076	.	1661	Q68DN1	CB016_HUMAN	R	1661	ENSP00000386190:S1661R	ENSP00000386190:S1661R	S	+	3	2	C2orf16	27657926	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.378000	0.00492	-0.487000	0.06735	-2.225000	0.00294	AGC		0.582	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		15	111	1	0	4.14922e-12	1	4.40068e-12	15	111				
TRAF2	7186	broad.mit.edu	37	9	139820173	139820173	+	Silent	SNP	C	C	T	rs560077345		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr9:139820173C>T	ENST00000247668.2	+	11	1378	c.1326C>T	c.(1324-1326)caC>caT	p.H442H	TRAF2_ENST00000536468.1_Silent_p.H442H|TRAF2_ENST00000359662.3_Silent_p.H494H	NM_021138.3	NP_066961.2	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	442	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein complex assembly (GO:0043623)|cellular response to nitric oxide (GO:0071732)|innate immune response (GO:0045087)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron death (GO:1901215)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|programmed necrotic cell death (GO:0097300)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein complex assembly (GO:0006461)|protein heterooligomerization (GO:0051291)|protein homotrimerization (GO:0070207)|protein K63-linked ubiquitination (GO:0070534)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of immunoglobulin secretion (GO:0051023)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|membrane raft (GO:0045121)|ubiquitin ligase complex (GO:0000151)	CD40 receptor binding (GO:0005174)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein phosphatase binding (GO:0019903)|signal transducer activity (GO:0004871)|sphingolipid binding (GO:0046625)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)		ACCGGGAGCACGTGATTGACG	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		19017	0.001		0.0	False		,,,				2504	0.0					ENST00000359662.3																			0				breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						c.(1480-1482)caC>caT		TNF receptor-associated factor 2							97.0	73.0	81.0					9																	139820173		2203	4300	6503	SO:0001819	synonymous_variant	7186				activation of caspase activity|activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cellular protein complex assembly|induction of apoptosis by extracellular signals|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|protein autoubiquitination|protein homotrimerization|protein K63-linked ubiquitination|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane	CD40 receptor binding|enzyme binding|protein binding|signal transducer activity|sphingolipid binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr9:139820173C>T	U12597	CCDS7013.1	9q34	2013-01-09			ENSG00000127191	ENSG00000127191		"""RING-type (C3HC4) zinc fingers"""	12032	protein-coding gene	gene with protein product		601895				7639698	Standard	NM_021138		Approved	TRAP3	uc004cjv.3	Q12933	OTTHUMG00000020952	ENST00000247668.2:c.1326C>T	9.37:g.139820173C>T			Somatic				TRAF2_ENST00000247668.2_Silent_p.H442H|TRAF2_ENST00000536468.1_Silent_p.H442H	p.H494H			WXS	Illumina GAIIx	Phase_I	Q12933	TRAF2_HUMAN	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)	11	1527	+	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	442			MATH.		A8K107|B4DPJ7|Q7Z337|Q96NT2	Silent	SNP	ENST00000247668.2	37	c.1482C>T	CCDS7013.1																																																																																				0.602	TRAF2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055166.1	NM_021138		18	33	0	0	0	1	0	18	33				
RYR3	6263	broad.mit.edu	37	15	34103222	34103222	+	Nonsense_Mutation	SNP	T	T	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr15:34103222T>A	ENST00000389232.4	+	72	10311	c.10241T>A	c.(10240-10242)tTg>tAg	p.L3414*	RYR3_ENST00000415757.3_Nonsense_Mutation_p.L3409*	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3414					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CGGAACAACTTGCACTTGCAG	0.478																																						ENST00000389232.4																			0				NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311						c.(10240-10242)tTg>tAg		ryanodine receptor 3							46.0	45.0	46.0					15																	34103222		1984	4170	6154	SO:0001587	stop_gained	6263				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr15:34103222T>A		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10241T>A	15.37:g.34103222T>A	ENSP00000373884:p.Leu3414*		Somatic				RYR3_ENST00000415757.3_Nonsense_Mutation_p.L3409*	p.L3414*	NM_001036.3	NP_001027.3	WXS	Illumina GAIIx	Phase_I	Q15413	RYR3_HUMAN		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	72	10311	+		all_lung(180;7.18e-09)	3414					O15175|Q15412	Nonsense_Mutation	SNP	ENST00000389232.4	37	c.10241T>A	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	53	20.138827	0.99927	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	.	.	.	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6314	0.76912	0.0:0.0:0.0:1.0	.	.	.	.	X	3414;3414;3409	.	ENSP00000354735:L3409X	L	+	2	0	RYR3	31890514	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.431000	0.80335	2.094000	0.63399	0.459000	0.35465	TTG		0.478	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			3	5	0	0	0	1	0	3	5				
KRT32	3882	broad.mit.edu	37	17	39620401	39620401	+	Nonsense_Mutation	SNP	G	G	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr17:39620401G>A	ENST00000225899.3	-	5	1028	c.925C>T	c.(925-927)Cag>Tag	p.Q309*		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	309	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				ATGTCTGACTGGTAGTTCTGA	0.577																																						ENST00000225899.3																			0				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						c.(925-927)Cag>Tag		keratin 32							177.0	133.0	148.0					17																	39620401		2203	4300	6503	SO:0001587	stop_gained	3882				epidermis development	intermediate filament	protein binding|structural molecule activity	g.chr17:39620401G>A	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.925C>T	17.37:g.39620401G>A	ENSP00000225899:p.Gln309*		Somatic					p.Q309*	NM_002278.3	NP_002269.3	WXS	Illumina GAIIx	Phase_I	Q14532	K1H2_HUMAN			5	1028	-		Breast(137;0.000812)	309			Coil 2.|Rod.			Nonsense_Mutation	SNP	ENST00000225899.3	37	c.925C>T	CCDS11393.1	.	.	.	.	.	.	.	.	.	.	G	36	5.782073	0.96937	.	.	ENSG00000108759	ENST00000225899	.	.	.	5.04	5.04	0.67666	.	0.000000	0.37348	N	0.002139	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	13.4096	0.60935	0.0:0.0:0.8328:0.1672	.	.	.	.	X	309	.	ENSP00000225899:Q309X	Q	-	1	0	KRT32	36873927	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.284000	0.43478	2.492000	0.84095	0.655000	0.94253	CAG		0.577	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278		19	24	0	0	0	1	0	19	24				
POM121L9P	29774	broad.mit.edu	37	22	24659591	24659591	+	RNA	SNP	A	A	G			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr22:24659591A>G	ENST00000414583.2	+	0	3116					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		ACTCACTGACATCGAAGGCTG	0.632																																						ENST00000414583.2																			0																																																			0							g.chr22:24659591A>G	AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659591A>G			Somatic						NR_003714.1		WXS	Illumina GAIIx	Phase_I					0	3116	+									RNA	SNP	ENST00000414583.2	37																																																																																						0.632	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1	NM_014549		3	15	0	0	0	1	0	3	15				
SCN11A	11280	broad.mit.edu	37	3	38913708	38913708	+	Silent	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr3:38913708C>T	ENST00000302328.3	-	20	3669	c.3471G>A	c.(3469-3471)gcG>gcA	p.A1157A	SCN11A_ENST00000450244.1_Silent_p.A1157A|SCN11A_ENST00000456224.3_Silent_p.A1119A|SCN11A_ENST00000444237.2_Silent_p.A1157A	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1157					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ACTGGGACAGCGCACGAAGAG	0.478																																						ENST00000450244.1																			0				NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119						c.(3469-3471)gcG>gcA		sodium channel, voltage-gated, type XI, alpha subunit	Cocaine(DB00907)						163.0	158.0	160.0					3																	38913708		2203	4300	6503	SO:0001819	synonymous_variant	11280				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity	g.chr3:38913708C>T	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.3471G>A	3.37:g.38913708C>T			Somatic				SCN11A_ENST00000444237.2_Silent_p.A1157A|SCN11A_ENST00000456224.3_Silent_p.A1119A|SCN11A_ENST00000302328.3_Silent_p.A1157A	p.A1157A			WXS	Illumina GAIIx	Phase_I	Q9UI33	SCNBA_HUMAN		Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	20	3669	-			1157					A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	37	c.3471G>A	CCDS33737.1																																																																																				0.478	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		60	60	0	0	0	1	0	60	60				
KLHL15	80311	broad.mit.edu	37	X	24007013	24007013	+	Silent	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chrX:24007013C>T	ENST00000328046.8	-	4	1095	c.840G>A	c.(838-840)ccG>ccA	p.P280P		NM_030624.2	NP_085127.2	Q96M94	KLH15_HUMAN	kelch-like family member 15	280					protein ubiquitination (GO:0016567)					autonomic_ganglia(1)|breast(1)|endometrium(8)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	22						CTGTAGTTTGCGGTTTTGCAG	0.433																																						ENST00000328046.8																			0				autonomic_ganglia(1)|breast(1)|endometrium(8)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	22						c.(838-840)ccG>ccA		kelch-like family member 15							108.0	101.0	103.0					X																	24007013		2203	4300	6503	SO:0001819	synonymous_variant	80311							g.chrX:24007013C>T	AB051464	CCDS35217.1	Xp22.1-p21	2013-01-30	2013-01-30		ENSG00000174010	ENSG00000174010		"""Kelch-like"", ""BTB/POZ domain containing"""	29347	protein-coding gene	gene with protein product			"""kelch-like 15 (Drosophila)"""			11214970, 14702039	Standard	NM_030624		Approved	KIAA1677	uc004dba.4	Q96M94	OTTHUMG00000021261	ENST00000328046.8:c.840G>A	X.37:g.24007013C>T			Somatic					p.P280P	NM_030624.2	NP_085127.2	WXS	Illumina GAIIx	Phase_I	Q96M94	KLH15_HUMAN			4	1095	-			280					Q32MN3|Q8NDA3|Q96BM6|Q9C0I6	Silent	SNP	ENST00000328046.8	37	c.840G>A	CCDS35217.1																																																																																				0.433	KLHL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056078.1	XM_040383		4	141	0	0	0	1	0	4	141				
TRIM49C	642612	broad.mit.edu	37	11	89774252	89774252	+	Missense_Mutation	SNP	G	G	A	rs201409537		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr11:89774252G>A	ENST00000448984.1	+	8	1222	c.893G>A	c.(892-894)aGt>aAt	p.S298N	TRIM49C_ENST00000432771.1_Intron	NM_001195234.1	NP_001182163.1	P0CI26	TR49C_HUMAN	tripartite motif containing 49C	298	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.S298N(4)		endometrium(3)|kidney(1)|lung(4)	8						GAAGCCAACAGTGATATCTTT	0.323																																						ENST00000448984.1																			4	Substitution - Missense(4)	p.S298N(4)	endometrium(2)|kidney(2)	endometrium(3)|kidney(1)|lung(4)	8						c.(892-894)aGt>aAt		tripartite motif containing 49C																																				SO:0001583	missense	642612					intracellular	zinc ion binding	g.chr11:89774252G>A	BC126470	CCDS53694.1	11q14.3	2014-02-17	2012-05-18	2012-05-18	ENSG00000204449	ENSG00000204449		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	38877	protein-coding gene	gene with protein product			"""tripartite motif containing 49-like 2"""	TRIM49L2			Standard	NM_001195234		Approved		uc010rua.2	P0CI26		ENST00000448984.1:c.893G>A	11.37:g.89774252G>A	ENSP00000388299:p.Ser298Asn		Somatic				TRIM49C_ENST00000432771.1_Intron	p.S298N	NM_001195234.1	NP_001182163.1	WXS	Illumina GAIIx	Phase_I	P0CI26	T49L2_HUMAN			8	1222	+			298			B30.2/SPRY.		A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Missense_Mutation	SNP	ENST00000448984.1	37	c.893G>A	CCDS53694.1	.	.	.	.	.	.	.	.	.	.	g	0.625	-0.819420	0.02776	.	.	ENSG00000204449	ENST00000448984	T	0.04809	3.55	0.823	-0.634	0.11516	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.04452	0.0122	L	0.52206	1.635	0.09310	N	1	B	0.12013	0.005	B	0.14023	0.01	T	0.43605	-0.9381	8	.	.	.	.	3.2016	0.06651	0.4432:0.0:0.5568:0.0	rs672762;rs9666958;rs16912727;rs672762	298	P0CI26	T49L2_HUMAN	N	298	ENSP00000388299:S298N	.	S	+	2	0	TRIM49L2	89413900	0.000000	0.05858	0.001000	0.08648	0.034000	0.12701	-1.058000	0.03482	-0.239000	0.09710	0.305000	0.20034	AGT		0.323	TRIM49C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395455.1	NM_001195234		4	52	0	0	0	1	0	4	52				
RNF43	54894	broad.mit.edu	37	17	56435332	56435332	+	Missense_Mutation	SNP	T	T	C			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr17:56435332T>C	ENST00000584437.1	-	8	3760	c.1805A>G	c.(1804-1806)aAc>aGc	p.N602S	RNF43_ENST00000583753.1_Missense_Mutation_p.N561S|RNF43_ENST00000577716.1_Missense_Mutation_p.N602S|RNF43_ENST00000407977.2_Missense_Mutation_p.N602S|RNF43_ENST00000500597.2_Missense_Mutation_p.N561S|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000581868.1_Missense_Mutation_p.N475S|RNF43_ENST00000577625.1_Missense_Mutation_p.N475S			Q68DV7	RNF43_HUMAN	ring finger protein 43	602	Pro-rich.				negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGCTGCTGAGTTGGATCTGGT	0.657																																						ENST00000584437.1																			0				NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60						c.(1804-1806)aAc>aGc		ring finger protein 43							57.0	69.0	65.0					17																	56435332		2203	4299	6502	SO:0001583	missense	54894					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding	g.chr17:56435332T>C		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.1805A>G	17.37:g.56435332T>C	ENSP00000463069:p.Asn602Ser		Somatic				RNF43_ENST00000577716.1_Missense_Mutation_p.N602S|RNF43_ENST00000500597.2_Missense_Mutation_p.N561S|RNF43_ENST00000577625.1_Missense_Mutation_p.N475S|RNF43_ENST00000583753.1_Missense_Mutation_p.N561S|RNF43_ENST00000581868.1_Missense_Mutation_p.N475S|RNF43_ENST00000407977.2_Missense_Mutation_p.N602S|BZRAP1-AS1_ENST00000583841.1_RNA	p.N602S			WXS	Illumina GAIIx	Phase_I	Q68DV7	RNF43_HUMAN			8	3760	-	Medulloblastoma(34;0.127)|all_neural(34;0.237)		602			Pro-rich.		A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	c.1805A>G	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	T	2.674	-0.276978	0.05679	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.16897	2.31;2.31	5.18	-1.62	0.08372	.	1.287800	0.04918	N	0.454417	T	0.06872	0.0175	N	0.14661	0.345	0.09310	N	1	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.06405	0.001;0.002;0.0	T	0.27297	-1.0078	10	0.05833	T	0.94	-9.4984	0.8	0.01074	0.1725:0.2915:0.1572:0.3788	.	561;602;602	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	S	602;561	ENSP00000385328:N602S;ENSP00000441969:N561S	ENSP00000385328:N602S	N	-	2	0	RNF43	53790331	0.814000	0.29104	0.003000	0.11579	0.140000	0.21249	0.357000	0.20199	0.006000	0.14734	0.172000	0.16884	AAC		0.657	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763		43	72	0	0	0	1	0	43	72				
GNAQ	2776	broad.mit.edu	37	9	80409488	80409488	+	Missense_Mutation	SNP	T	T	G	rs121913492		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr9:80409488T>G	ENST00000286548.4	-	5	848	c.626A>C	c.(625-627)cAa>cCa	p.Q209P	GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7P	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	209			Q -> L (found in blue naevi and uveal melanoma samples; somatic mutation; constitutive activation).		action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.Q209L(87)|p.Q209P(64)|p.Q209Y(1)|p.Q209R(1)		NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						CTCTGACCTTTGGCCCCCTAC	0.348			Mis		uveal melanoma																																	ENST00000286548.4				Dom	yes		9	9q21	2776	Mis	"""guanine nucleotide binding protein (G protein), q polypeptide"""			E			uveal melanoma		153	Substitution - Missense(153)	p.Q209L(87)|p.Q209P(64)|p.Q209Y(1)|p.Q209R(1)	eye(99)|skin(43)|meninges(10)|NS(1)	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						c.(625-627)cAa>cCa		guanine nucleotide binding protein (G protein), q polypeptide							108.0	105.0	106.0					9																	80409488		2203	4300	6503	SO:0001583	missense	2776				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	g.chr9:80409488T>G		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052			4390	protein-coding gene	gene with protein product		600998				8825633	Standard	NM_002072		Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.626A>C	9.37:g.80409488T>G	ENSP00000286548:p.Gln209Pro		Somatic				GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7P	p.Q209P	NM_002072.3	NP_002063.2	WXS	Illumina GAIIx	Phase_I	P50148	GNAQ_HUMAN			5	848	-			209					O15108|Q13462|Q6NT27|Q92471|Q9BZB9	Missense_Mutation	SNP	ENST00000286548.4	37	c.626A>C	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614273	0.87359	.	.	ENSG00000156052	ENST00000286548;ENST00000397476	D;D	0.91237	-2.81;-2.81	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97164	0.9073	H	0.97291	3.975	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.98607	1.0661	10	0.87932	D	0	.	15.9502	0.79827	0.0:0.0:0.0:1.0	.	209	P50148	GNAQ_HUMAN	P	209;7	ENSP00000286548:Q209P;ENSP00000443197:Q7P	ENSP00000286548:Q209P	Q	-	2	0	GNAQ	79599308	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.040000	0.89188	2.167000	0.68274	0.460000	0.39030	CAA		0.348	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1	NM_002072		41	35	0	0	0	1	0	41	35				
THOC2	57187	broad.mit.edu	37	X	122769935	122769935	+	Silent	SNP	G	G	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chrX:122769935G>T	ENST00000245838.8	-	19	2044	c.2013C>A	c.(2011-2013)ggC>ggA	p.G671G	THOC2_ENST00000491737.1_Silent_p.G556G|THOC2_ENST00000355725.4_Silent_p.G671G	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	671					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						AATACCTTTTGCCCGCCTTTA	0.363																																						ENST00000245838.8																			0				breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						c.(2011-2013)ggC>ggA		THO complex 2							92.0	77.0	81.0					X																	122769935		1822	4075	5897	SO:0001819	synonymous_variant	57187				intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding	g.chrX:122769935G>T	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"""THO complex subunits"""	19073	protein-coding gene	gene with protein product		300395	"""chromosome X open reading frame 3"""	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.2013C>A	X.37:g.122769935G>T			Somatic				THOC2_ENST00000355725.4_Silent_p.G671G|THOC2_ENST00000491737.1_Silent_p.G556G	p.G671G	NM_001081550.1	NP_001075019.1	WXS	Illumina GAIIx	Phase_I	Q8NI27	THOC2_HUMAN			19	2044	-			671					A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	37	c.2013C>A	CCDS43988.1																																																																																				0.363	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			36	38	1	0	5.43694e-19	1	5.94665e-19	36	38				
NPEPL1	79716	broad.mit.edu	37	20	57276201	57276201	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr20:57276201G>A	ENST00000356091.6	+	6	1097	c.809G>A	c.(808-810)aGc>aAc	p.S270N	NPEPL1_ENST00000525967.1_Missense_Mutation_p.S242N|NPEPL1_ENST00000525817.1_Missense_Mutation_p.S222N|STX16-NPEPL1_ENST00000530122.1_3'UTR	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	270						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			GGAGGCCTCAGCATCAAAGGG	0.687																																						ENST00000356091.6																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14						c.(808-810)aGc>aAc		aminopeptidase-like 1							24.0	24.0	24.0					20																	57276201		2037	4189	6226	SO:0001583	missense	79716				proteolysis	cytoplasm	aminopeptidase activity|manganese ion binding|metalloexopeptidase activity	g.chr20:57276201G>A	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.809G>A	20.37:g.57276201G>A	ENSP00000348395:p.Ser270Asn		Somatic				NPEPL1_ENST00000525967.1_Missense_Mutation_p.S242N|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525817.1_Missense_Mutation_p.S222N	p.S270N	NM_024663.3	NP_078939.3	WXS	Illumina GAIIx	Phase_I	Q8NDH3	PEPL1_HUMAN	BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)		6	1097	+	all_lung(29;0.0175)		270					A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	37	c.809G>A	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.668192	0.88348	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.48201	0.82;0.82;0.82	5.01	5.01	0.66863	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.66025	0.2748	M	0.66939	2.045	0.80722	D	1	D;D;D;D	0.89917	0.998;0.997;1.0;0.961	D;D;D;P	0.81914	0.985;0.975;0.995;0.835	T	0.65829	-0.6073	10	0.41790	T	0.15	-41.2309	15.4714	0.75441	0.0:0.0:1.0:0.0	.	270;222;242;270	Q8NDH3;G5EA34;E9PN47;Q8NDH3-3	PEPL1_HUMAN;.;.;.	N	242;222;270	ENSP00000434810:S242N;ENSP00000437112:S222N;ENSP00000348395:S270N	ENSP00000348395:S270N	S	+	2	0	NPEPL1	56709608	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.375000	0.97178	2.313000	0.78055	0.585000	0.79938	AGC		0.687	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		5	3	0	0	0	1	0	5	3				
C7orf55	154791	broad.mit.edu	37	7	139026134	139026134	+	Missense_Mutation	SNP	G	G	A	rs75669887		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr7:139026134G>A	ENST00000297534.6	+	1	257	c.4G>A	c.(4-6)Gcg>Acg	p.A2T	C7orf55-LUC7L2_ENST00000541170.3_Intron|LUC7L2_ENST00000541515.3_Missense_Mutation_p.A2T|C7orf55_ENST00000481123.1_Intron	NM_197964.4	NP_932068.2	Q96HJ9	CG055_HUMAN	chromosome 7 open reading frame 55	2						mitochondrion (GO:0005739)				breast(1)|lung(2)	3						CAGGACAATGGCGGCCTTAGG	0.657											OREG0018357	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		15526	0.0		0.001	False		,,,				2504	0.0					ENST00000541515.3																			0				NS(2)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	16						c.(4-6)Gcg>Acg		LUC7-like 2 (S. cerevisiae)							54.0	63.0	60.0					7																	139026134		2203	4300	6503	SO:0001583	missense	51631						enzyme binding|metal ion binding	g.chr7:139026134G>A	AF161386	CCDS5853.1	7q34	2009-01-22	2009-01-22	2009-01-22	ENSG00000164898	ENSG00000164898			26946	protein-coding gene	gene with protein product	"""formation of mitochondrial complexes 1 homolog (S. cerevisiae)"""					12477932	Standard	NM_197964		Approved	HSPC268, FMC1		Q96HJ9	OTTHUMG00000151719	ENST00000297534.6:c.4G>A	7.37:g.139026134G>A	ENSP00000297534:p.Ala2Thr		Somatic	OREG0018357	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1645	C7orf55-LUC7L2_ENST00000541170.3_Intron|C7orf55_ENST00000297534.6_Missense_Mutation_p.A2T|C7orf55_ENST00000481123.1_Intron	p.A2T	NM_001244584.2	NP_001231513.1	WXS	Illumina GAIIx	Phase_I	Q9Y383	LC7L2_HUMAN			1	29	+	Melanoma(164;0.242)		0					B7Z4Q3|Q75M90|Q9P0B3	Missense_Mutation	SNP	ENST00000297534.6	37	c.4G>A	CCDS5853.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	24.4	4.529993	0.85706	.	.	ENSG00000164898;ENSG00000146963	ENST00000297534;ENST00000541515	T;T	0.53640	0.61;1.28	5.46	4.58	0.56647	.	0.067803	0.56097	D	0.000025	T	0.48205	0.1487	M	0.68593	2.085	0.49130	D	0.999758	B;B	0.22746	0.02;0.074	B;B	0.20955	0.006;0.032	T	0.51593	-0.8686	10	0.72032	D	0.01	-0.0343	14.2126	0.65773	0.0713:0.0:0.9287:0.0	.	2;2	B7Z4Q3;Q96HJ9	.;CG055_HUMAN	T	2	ENSP00000297534:A2T;ENSP00000440222:A2T	ENSP00000297534:A2T	A	+	1	0	LUC7L2;C7orf55	138676674	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.514000	0.60482	1.546000	0.49388	0.591000	0.81541	GCG		0.657	C7orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323626.1	NM_197964		20	28	0	0	0	1	0	20	28				
SAP130	79595	broad.mit.edu	37	2	128775359	128775359	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr2:128775359C>A	ENST00000259235.3	-	3	450	c.321G>T	c.(319-321)ttG>ttT	p.L107F	SAP130_ENST00000259234.6_Missense_Mutation_p.L81F|SAP130_ENST00000357702.5_Missense_Mutation_p.L107F	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	107					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		GGTGTGTCGACAACATCTGCA	0.582																																						ENST00000357702.5																			0				NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45						c.(319-321)ttG>ttT		Sin3A-associated protein, 130kDa							149.0	126.0	134.0					2																	128775359		2203	4300	6503	SO:0001583	missense	79595				histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity	g.chr2:128775359C>A	BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"""sin3A-associated protein, 130kDa"""			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.321G>T	2.37:g.128775359C>A	ENSP00000259235:p.Leu107Phe		Somatic				SAP130_ENST00000259234.6_Missense_Mutation_p.L81F|SAP130_ENST00000259235.3_Missense_Mutation_p.L107F	p.L107F	NM_001145928.1	NP_001139400.1	WXS	Illumina GAIIx	Phase_I	Q9H0E3	SP130_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0771)	3	452	-	Colorectal(110;0.1)		107					B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Missense_Mutation	SNP	ENST00000259235.3	37	c.321G>T	CCDS2153.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.238823	0.58995	.	.	ENSG00000136715	ENST00000357702;ENST00000259235;ENST00000259234;ENST00000424298;ENST00000450957	.	.	.	5.79	4.92	0.64577	.	0.247403	0.34750	N	0.003714	T	0.59824	0.2222	L	0.32530	0.975	0.44515	D	0.99746	P;D;D	0.71674	0.487;0.997;0.998	B;D;D	0.65010	0.189;0.931;0.914	T	0.54655	-0.8261	9	0.09084	T	0.74	-9.8508	13.0129	0.58741	0.0:0.9254:0.0:0.0746	.	107;81;107	B7ZLM3;Q96DP1;Q9H0E3	.;.;SP130_HUMAN	F	107;107;81;81;81	.	ENSP00000259234:L81F	L	-	3	2	SAP130	128491829	1.000000	0.71417	0.994000	0.49952	0.719000	0.41307	5.228000	0.65310	1.442000	0.47568	0.585000	0.79938	TTG		0.582	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545		36	64	1	0	3.93418e-24	1	4.44182e-24	36	64				
SF3B1	23451	broad.mit.edu	37	2	198267484	198267484	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr2:198267484G>A	ENST00000335508.6	-	14	1964	c.1873C>T	c.(1873-1875)Cgt>Tgt	p.R625C	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	625					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.R625C(5)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GTTGTGTTACGGACATACTCA	0.433			Mis		myelodysplastic syndrome																																	ENST00000335508.6				Dom	yes		2	2q33.1	23451	Mis	"""splicing factor 3b, subunit 1, 155kDa"""			L			myelodysplastic syndrome		5	Substitution - Missense(5)	p.R625C(5)	haematopoietic_and_lymphoid_tissue(5)	NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633						c.(1873-1875)Cgt>Tgt		splicing factor 3b, subunit 1, 155kDa							93.0	90.0	91.0					2																	198267484		2203	4300	6503	SO:0001583	missense	23451				nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding	g.chr2:198267484G>A	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1873C>T	2.37:g.198267484G>A	ENSP00000335321:p.Arg625Cys		Somatic					p.R625C	NM_012433.2	NP_036565.2	WXS	Illumina GAIIx	Phase_I	O75533	SF3B1_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.246)		14	1964	-								E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	c.1873C>T	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.873082	0.72180	.	.	ENSG00000115524	ENST00000335508	T	0.74421	-0.84	5.82	4.93	0.64822	Armadillo-like helical (1);Armadillo-type fold (1);	0.053241	0.64402	D	0.000001	D	0.90331	0.6975	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.93337	0.6706	10	0.87932	D	0	.	15.2676	0.73675	0.0:0.0:0.7451:0.2549	.	625	O75533	SF3B1_HUMAN	C	625	ENSP00000335321:R625C	ENSP00000335321:R625C	R	-	1	0	SF3B1	197975729	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.689000	0.61723	1.444000	0.47605	-0.182000	0.12963	CGT		0.433	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			21	32	0	0	0	1	0	21	32				
ZNRD1-AS1	80862	broad.mit.edu	37	6	29977327	29977327	+	RNA	SNP	T	T	C	rs200662795		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr6:29977327T>C	ENST00000376797.3	-	0	731				ZNRD1-AS1_ENST00000448093.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000444051.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		GACAGCTGCCTTGTGTGGGAC	0.438																																						ENST00000376797.3																			0																																																			0							g.chr6:29977327T>C	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.29977327T>C			Somatic				ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA				WXS	Illumina GAIIx	Phase_I					0	731	-									RNA	SNP	ENST00000376797.3	37																																																																																						0.438	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253083.1	NR_026751		3	70	0	0	0	1	0	3	70				
ZNRD1-AS1	80862	broad.mit.edu	37	6	29977342	29977342	+	RNA	SNP	A	A	T	rs113017032	byFrequency	TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr6:29977342A>T	ENST00000376797.3	-	0	731				ZNRD1-AS1_ENST00000448093.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000444051.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1																		TGGGACTGAGAGGCAAGATTT	0.438													A|||	16	0.00319489	0.003	0.0029	5008	,	,		21762	0.0		0.003	False		,,,				2504	0.0072					ENST00000376797.3																			0																																																			0							g.chr6:29977342A>T	AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623		"""Long non-coding RNAs"""	13924	non-coding RNA	RNA, long non-coding		615714	"""chromosome 6 open reading frame 12"", ""non-protein coding RNA 171"", ""ZNRD1 antisense RNA (non-protein coding)"", ""ZNRD1 antisense RNA 1 (non-protein coding)"""	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS		9553157, 11130983, 25110835	Standard	NR_026751		Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109		6.37:g.29977342A>T			Somatic				ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA				WXS	Illumina GAIIx	Phase_I					0	731	-									RNA	SNP	ENST00000376797.3	37																																																																																						0.438	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000253083.1	NR_026751		3	70	0	0	0	1	0	3	70				
OR6K3	391114	broad.mit.edu	37	1	158686997	158686997	+	Silent	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr1:158686997C>T	ENST00000368146.1	-	1	956	c.957G>A	c.(955-957)ctG>ctA	p.L319L	OR6K3_ENST00000368145.1_Silent_p.L303L			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	319						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					GAAGACAGAACAGTTTTTTAA	0.388																																						ENST00000368146.1																			0				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41						c.(955-957)ctG>ctA		olfactory receptor, family 6, subfamily K, member 3							125.0	128.0	127.0					1																	158686997		2203	4300	6503	SO:0001819	synonymous_variant	391114				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:158686997C>T	AB065633	CCDS30903.1, CCDS30903.2	1q23.1	2012-08-09			ENSG00000203757	ENSG00000203757		"""GPCR / Class A : Olfactory receptors"""	15030	protein-coding gene	gene with protein product							Standard	NM_001005327		Approved		uc021pbn.1	Q8NGY3	OTTHUMG00000022770	ENST00000368146.1:c.957G>A	1.37:g.158686997C>T			Somatic				OR6K3_ENST00000368145.1_Silent_p.L303L	p.L319L			WXS	Illumina GAIIx	Phase_I	Q8NGY3	OR6K3_HUMAN			1	956	-	all_hematologic(112;0.0378)		319					Q5VUV0|Q6IFR5	Silent	SNP	ENST00000368146.1	37	c.957G>A																																																																																					0.388	OR6K3-201	KNOWN	basic	protein_coding	protein_coding				33	36	0	0	0	1	0	33	36				
ROS1	6098	broad.mit.edu	37	6	117710788	117710788	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr6:117710788G>A	ENST00000368508.3	-	12	1682	c.1484C>T	c.(1483-1485)cCc>cTc	p.P495L	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.P504L	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	495					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		ATCAGCAAAGGGGATGCGAGG	0.423			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																	ENST00000368508.3				Dom	yes		6	6q22	6098	T	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)			"""O, E"""	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""		"""glioblastoma, NSCLC"""	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	0				NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162						c.(1483-1485)cCc>cTc		c-ros oncogene 1 , receptor tyrosine kinase							90.0	81.0	84.0					6																	117710788		2203	4300	6503	SO:0001583	missense	6098				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity	g.chr6:117710788G>A	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.1484C>T	6.37:g.117710788G>A	ENSP00000357494:p.Pro495Leu		Somatic				ROS1_ENST00000368507.3_Missense_Mutation_p.P504L|GOPC_ENST00000467125.1_Intron	p.P495L	NM_002944.2	NP_002935.2	WXS	Illumina GAIIx	Phase_I	P08922	ROS_HUMAN		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)	12	1682	-		all_cancers(87;0.00846)|all_epithelial(87;0.0242)	495					Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	c.1484C>T	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	G	9.247	1.039770	0.19669	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	D;D	0.90900	-2.75;-2.75	5.92	4.12	0.48240	.	0.571379	0.17934	N	0.157078	T	0.74550	0.3731	N	0.24115	0.695	0.46701	D	0.999164	B	0.09022	0.002	B	0.06405	0.002	T	0.71553	-0.4558	10	0.66056	D	0.02	.	9.5245	0.39156	0.0748:0.1426:0.7826:0.0	.	495	P08922	ROS1_HUMAN	L	495;504	ENSP00000357494:P495L;ENSP00000357493:P504L	ENSP00000357493:P504L	P	-	2	0	ROS1	117817481	0.998000	0.40836	0.183000	0.23137	0.044000	0.14063	2.718000	0.47236	0.829000	0.34733	0.561000	0.74099	CCC		0.423	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			19	1	0	0	0	1	0	19	1				
TAF15	8148	broad.mit.edu	37	17	34173974	34173974	+	Silent	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr17:34173974C>T	ENST00000592237.1	+	19	1747	c.1218C>T	c.(1216-1218)gtC>gtT	p.V406V	TAF15_ENST00000311979.3_3'UTR|TAF15_ENST00000588240.1_3'UTR			Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		GTTCCTTTGTCTCTGACATGA	0.393			T	"""TEC, CHN1, ZNF384"""	"""extraskeletal myxoid chondrosarcomas, ALL"""																																	ENST00000592237.1				Dom	yes		17	17q11.1-q11.2	8148	T	"""TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"""			"""L, M"""	"""TEC, CHN1, ZNF384"""		"""extraskeletal myxoid chondrosarcomas, ALL"""	TAF15/NR4A3(33)	0				lung(1)|ovary(1)|skin(2)|stomach(1)	5						c.(1216-1218)gtC>gtT		TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa							115.0	108.0	111.0					17																	34173974		2203	4300	6503	SO:0001819	synonymous_variant	8148				positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding	g.chr17:34173974C>T	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"""RNA binding motif (RRM) containing"""	11547	protein-coding gene	gene with protein product		601574	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"""	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000592237.1:c.1218C>T	17.37:g.34173974C>T			Somatic				TAF15_ENST00000311979.3_3'UTR|TAF15_ENST00000588240.1_3'UTR	p.V406V			WXS	Illumina GAIIx	Phase_I	Q92804	RBP56_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)	19	1747	+		Ovarian(249;0.17)	0			Arg/Gly-rich.		D3DPM5|Q15775|Q5T077	Silent	SNP	ENST00000592237.1	37	c.1218C>T																																																																																					0.393	TAF15-006	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000449142.1	NM_139215		28	27	0	0	0	1	0	28	27				
GTDC1	79712	broad.mit.edu	37	2	144966218	144966218	+	Missense_Mutation	SNP	G	G	A	rs115723847		TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr2:144966218G>A	ENST00000392869.2	-	3	283	c.131C>T	c.(130-132)aCa>aTa	p.T44I	GTDC1_ENST00000463875.2_Intron|GTDC1_ENST00000542155.1_Missense_Mutation_p.T44I|GTDC1_ENST00000409298.1_Missense_Mutation_p.T44I|GTDC1_ENST00000467352.1_5'Flank|GTDC1_ENST00000241391.5_Missense_Mutation_p.T44I|GTDC1_ENST00000344850.4_Missense_Mutation_p.T44I|GTDC1_ENST00000392867.3_Missense_Mutation_p.T44I|GTDC1_ENST00000409214.1_Missense_Mutation_p.T44I	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	44					biosynthetic process (GO:0009058)		transferase activity, transferring glycosyl groups (GO:0016757)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.0914)		TAAAGCAGATGTCCGGGCTCT	0.428													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16013	0.0		0.0	False		,,,				2504	0.0					ENST00000392869.2																			0				central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25						c.(130-132)aCa>aTa		glycosyltransferase-like domain containing 1							86.0	86.0	86.0					2																	144966218		2203	4300	6503	SO:0001583	missense	79712				biosynthetic process		transferase activity, transferring glycosyl groups	g.chr2:144966218G>A	AY281366	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	2q22.3	2013-02-22			ENSG00000121964	ENSG00000121964		"""Glycosyltransferase group 1 domain containing"""	20887	protein-coding gene	gene with protein product	"""mannosyltransferase-like"""	610165				15068588, 21821951	Standard	NM_024659		Approved	FLJ11753, Hmat-Xa	uc010fnn.3	Q4AE62	OTTHUMG00000131835	ENST00000392869.2:c.131C>T	2.37:g.144966218G>A	ENSP00000376608:p.Thr44Ile		Somatic				GTDC1_ENST00000409214.1_Missense_Mutation_p.T44I|GTDC1_ENST00000392867.3_Missense_Mutation_p.T44I|GTDC1_ENST00000542155.1_Missense_Mutation_p.T44I|GTDC1_ENST00000241391.5_Missense_Mutation_p.T44I|GTDC1_ENST00000409298.1_Missense_Mutation_p.T44I|GTDC1_ENST00000344850.4_Missense_Mutation_p.T44I|GTDC1_ENST00000463875.2_Intron	p.T44I	NM_001284234.1	NP_001271163.1	WXS	Illumina GAIIx	Phase_I	Q4AE62	GTDC1_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0914)	3	283	-								A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Missense_Mutation	SNP	ENST00000392869.2	37	c.131C>T	CCDS33300.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	25.7	4.666378	0.88251	.	.	ENSG00000121964	ENST00000392869;ENST00000409214;ENST00000392867;ENST00000409298;ENST00000542155;ENST00000241391;ENST00000344850;ENST00000437114;ENST00000417450	T;T;T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97	6.08	6.08	0.98989	Glycosyltransferase family 1, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.67813	0.2933	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	0.958;1.0;1.0;1.0	P;D;D;D	0.91635	0.693;0.993;0.999;0.991	T	0.65660	-0.6114	10	0.52906	T	0.07	0.0079	20.6634	0.99662	0.0:0.0:1.0:0.0	.	44;44;44;44	Q4AE62-2;B8ZZ45;Q4AE62;Q4AE62-3	.;.;GTDC1_HUMAN;.	I	44	ENSP00000376608:T44I;ENSP00000386581:T44I;ENSP00000376606:T44I;ENSP00000386691:T44I;ENSP00000438323:T44I;ENSP00000241391:T44I;ENSP00000339750:T44I;ENSP00000403869:T44I;ENSP00000400661:T44I	ENSP00000241391:T44I	T	-	2	0	GTDC1	144682688	1.000000	0.71417	0.982000	0.44146	0.852000	0.48524	9.320000	0.96346	2.894000	0.99253	0.655000	0.94253	ACA		0.428	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2	NM_024659		8	38	0	0	0	1	0	8	38				
KIAA1024	23251	broad.mit.edu	37	15	79760547	79760547	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr15:79760547C>T	ENST00000305428.3	+	4	2647	c.2572C>T	c.(2572-2574)Cca>Tca	p.P858S		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	858						integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						ATCTTTAAACCCAAATAATTT	0.388																																						ENST00000305428.3																			0				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						c.(2572-2574)Cca>Tca		KIAA1024							38.0	34.0	35.0					15																	79760547		2196	4293	6489	SO:0001583	missense	23251					integral to membrane		g.chr15:79760547C>T	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.2572C>T	15.37:g.79760547C>T	ENSP00000307461:p.Pro858Ser		Somatic					p.P858S	NM_015206.2	NP_056021.1	WXS	Illumina GAIIx	Phase_I	Q9UPX6	K1024_HUMAN			4	2647	+			858					A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	c.2572C>T	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812684	0.70912	.	.	ENSG00000169330	ENST00000305428	T	0.63744	-0.06	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.78898	0.4356	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77088	-0.2717	9	.	.	.	.	19.7863	0.96440	0.0:1.0:0.0:0.0	.	858	Q9UPX6	K1024_HUMAN	S	858	ENSP00000307461:P858S	.	P	+	1	0	KIAA1024	77547602	1.000000	0.71417	1.000000	0.80357	0.209000	0.24338	7.456000	0.80751	2.665000	0.90641	0.655000	0.94253	CCA		0.388	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		13	18	0	0	0	1	0	13	18				
PRSS50	29122	broad.mit.edu	37	3	46755884	46755901	+	In_Frame_Del	DEL	CGGTACCTGCTATGCATG	CGGTACCTGCTATGCATG	-	rs201421841|rs142097717	byFrequency	TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr3:46755884_46755901delCGGTACCTGCTATGCATG	ENST00000460241.1	-	9	2231_2248	c.561_578delCATGCATAGCAGGTACCG	c.(559-579)atcatgcatagcaggtaccgg>atg	p.187_193IMHSRYR>M	PRSS50_ENST00000315170.7_In_Frame_Del_p.187_193IMHSRYR>M			Q9UI38	TSP50_HUMAN	protease, serine, 50	187	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	serine-type endopeptidase activity (GO:0004252)|threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						CCGCTGGGCCCGGTACCTGCTATGCATGATGACCTGGA	0.61																																					Pancreas(41;915 1239 11561 17469)	ENST00000460241.1																			0				endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						c.(559-579)atcatgcatagcaggtaccgg>atg		protease, serine, 50																																				SO:0001651	inframe_deletion	29122				proteolysis	endoplasmic reticulum	serine-type endopeptidase activity|threonine-type endopeptidase activity	g.chr3:46755884_46755901delCGGTACCTGCTATGCATG	AF100707	CCDS2745.1	3p21.31	2011-05-24			ENSG00000206549	ENSG00000206549		"""Serine peptidases / Serine peptidases"""	17910	protein-coding gene	gene with protein product	"""cancer/testis antigen 20"", ""testes specific protease 50"""	607950				10397268	Standard	NM_013270		Approved	TSP50, CT20	uc003cqe.1	Q9UI38	OTTHUMG00000164067	ENST00000460241.1:c.561_578delCATGCATAGCAGGTACCG	3.37:g.46755884_46755901delCGGTACCTGCTATGCATG	ENSP00000418875:p.Ile187_Arg193delinsMet		Somatic				PRSS50_ENST00000315170.7_In_Frame_Del_p.187_193IMHSRYR>M	p.187_193IMHSRYR>M			WXS	Illumina GAIIx	Phase_I	Q9UI38	TSP50_HUMAN			9	2231_2248	-			187			Peptidase S1.			In_Frame_Del	DEL	ENST00000460241.1	37	c.561_578delCATGCATAGCAGGTACCG	CCDS2745.1																																																																																				0.610	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1			2	4						2	4	---	---	---	---
UBQLN3	50613	broad.mit.edu	37	11	5529918	5529920	+	In_Frame_Del	DEL	TGG	TGG	-	rs2234451	byFrequency	TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr11:5529918_5529920delTGG	ENST00000311659.4	-	2	1016_1018	c.869_871delCCA	c.(868-873)accagc>agc	p.T290del	HBG2_ENST00000380259.2_Intron	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	290			T -> S (in dbSNP:rs2234451).							NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAAGGTTGGCTGGTGGTGGTGGT	0.537																																					Ovarian(72;684 1260 12332 41642 52180)	ENST00000311659.4																			0				NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39						c.(868-873)accagc>agc		ubiquilin 3																																				SO:0001651	inframe_deletion	50613							g.chr11:5529918_5529920delTGG	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"""Ubiquilin family"""	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.869_871delCCA	11.37:g.5529927_5529929delTGG	ENSP00000347997:p.Thr290del		Somatic				HBG2_ENST00000380259.2_Intron	p.T290del	NM_017481.2	NP_059509.1	WXS	Illumina GAIIx	Phase_I	Q9H347	UBQL3_HUMAN		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	2	1016_1018	-		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)	290		T -> S (in dbSNP:rs2234451).			Q9NRE0	In_Frame_Del	DEL	ENST00000311659.4	37	c.869_871delCCA	CCDS7758.1																																																																																				0.537	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		7	90						7	90	---	---	---	---
ADRBK1	156	broad.mit.edu	37	11	67051341	67051342	+	Frame_Shift_Ins	INS	-	-	C			TCGA-VD-A8KB-01A-11D-A39W-08	TCGA-VD-A8KB-10C-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9baf009f-4121-4380-96f2-7458dc968b7e	4e2fc801-70e6-4d26-b168-ce1b3026ed5e	g.chr11:67051341_67051342insC	ENST00000308595.5	+	17	1702_1703	c.1412_1413insC	c.(1411-1416)atccccfs	p.IP471fs	ADRBK1_ENST00000527176.1_3'UTR|ADRBK1_ENST00000526285.1_Intron	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	471	AGC-kinase C-terminal.				activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	CCCCCGCTGATCCCCCCACGAG	0.634																																						ENST00000308595.5																			0				cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22						c.(1411-1416)atccccfs		adrenergic, beta, receptor kinase 1	Adenosine triphosphate(DB00171)																																			SO:0001589	frameshift_variant	156				activation of phospholipase C activity|cardiac muscle contraction|desensitization of G-protein coupled receptor protein signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of striated muscle contraction|negative regulation of the force of heart contraction by chemical signal|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of catecholamine secretion|tachykinin receptor signaling pathway	cytosol|soluble fraction	alpha-2A adrenergic receptor binding|ATP binding|beta-adrenergic receptor kinase activity|Edg-2 lysophosphatidic acid receptor binding|G-protein coupled receptor kinase activity|signal transducer activity	g.chr11:67051341_67051342insC	X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"""Pleckstrin homology (PH) domain containing"""	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.1418dupC	11.37:g.67051347_67051347dupC	ENSP00000312262:p.Ile471fs		Somatic				ADRBK1_ENST00000527176.1_3'UTR|ADRBK1_ENST00000526285.1_Intron	p.IP471fs	NM_001619.3	NP_001610.2	WXS	Illumina GAIIx	Phase_I	P25098	ARBK1_HUMAN	BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		17	1702_1703	+			471			AGC-kinase C-terminal.		B0ZBE1|Q13837|Q6GTT3	Frame_Shift_Ins	INS	ENST00000308595.5	37	c.1412_1413insC	CCDS8156.1																																																																																				0.634	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619		2	4						2	4	---	---	---	---
