#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	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
VPS53	55275	broad.mit.edu	37	17	465966	465966	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr17:465966C>T	ENST00000571805.1	-	14	1469	c.1333G>A	c.(1333-1335)Gat>Aat	p.D445N	VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000401468.3_Missense_Mutation_p.D168N|VPS53_ENST00000446250.2_Missense_Mutation_p.D247N|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000291074.5_Missense_Mutation_p.D416N|VPS53_ENST00000437048.2_Missense_Mutation_p.D445N			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	445					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		ACAAACCGATCTATCAGCTCT	0.458																																						ENST00000437048.2																			0				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19						c.(1333-1335)Gat>Aat		vacuolar protein sorting 53 homolog (S. cerevisiae)							53.0	50.0	51.0					17																	465966		2203	4300	6503	SO:0001583	missense	55275				protein transport	endosome membrane|Golgi apparatus		g.chr17:465966C>T		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"""vacuolar protein sorting 53 (yeast)"""			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.1333G>A	17.37:g.465966C>T	ENSP00000459312:p.Asp445Asn					VPS53_ENST00000571805.1_Missense_Mutation_p.D445N|VPS53_ENST00000446250.2_Missense_Mutation_p.D247N|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000401468.3_Missense_Mutation_p.D168N|VPS53_ENST00000291074.5_Missense_Mutation_p.D416N|VPS53_ENST00000576149.1_5'UTR	p.D445N	NM_001128159.2	NP_001121631.1	Q5VIR6	VPS53_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)	14	1479	-			445					A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Missense_Mutation	SNP	ENST00000571805.1	37	c.1333G>A		.	.	.	.	.	.	.	.	.	.	C	32	5.107423	0.94292	.	.	ENSG00000141252	ENST00000437048;ENST00000446250;ENST00000291074;ENST00000401468;ENST00000389040	T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.5	5.97	5.97	0.96955	Vps53-like, N-terminal (1);	0.041315	0.85682	D	0.000000	T	0.50137	0.1598	M	0.70595	2.14	0.80722	D	1	B;B;P;B;B	0.39601	0.097;0.218;0.68;0.179;0.332	B;B;P;B;P	0.44946	0.196;0.167;0.465;0.33;0.465	T	0.48603	-0.9021	10	0.59425	D	0.04	-23.5019	19.412	0.94677	0.0:1.0:0.0:0.0	.	168;445;247;445;416	E7EVT8;Q5VIR6-4;G3V0H8;Q5VIR6;Q5VIR6-2	.;.;.;VPS53_HUMAN;.	N	445;247;416;168;397	ENSP00000401435:D445N;ENSP00000394386:D247N;ENSP00000291074:D416N;ENSP00000384294:D168N;ENSP00000373692:D397N	ENSP00000291074:D416N	D	-	1	0	VPS53	412716	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.427000	0.80284	2.828000	0.97474	0.655000	0.94253	GAT		0.458	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289		4	64	0	0	0	1	0	4	64				
MMP13	4322	broad.mit.edu	37	11	102822797	102822797	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr11:102822797C>T	ENST00000260302.3	-	5	771	c.743G>A	c.(742-744)gGc>gAc	p.G248D	MMP13_ENST00000340273.4_Missense_Mutation_p.G248D	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	248					bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G248D(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	GTGGCTTTTGCCGGTGTAGGT	0.448																																						ENST00000260302.3																			1	Substitution - Missense(1)	p.G248D(1)	kidney(1)	NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27						c.(742-744)gGc>gAc		matrix metallopeptidase 13 (collagenase 3)							248.0	239.0	242.0					11																	102822797		2202	4299	6501	SO:0001583	missense	4322				collagen catabolic process|proteolysis	extracellular space	metalloendopeptidase activity|zinc ion binding	g.chr11:102822797C>T	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"""Endogenous ligands"""	7159	protein-coding gene	gene with protein product	"""collagenase 3"""	600108	"""matrix metalloproteinase 13 (collagenase 3)"""			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.743G>A	11.37:g.102822797C>T	ENSP00000260302:p.Gly248Asp					MMP13_ENST00000340273.4_Missense_Mutation_p.G248D	p.G248D	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN		BRCA - Breast invasive adenocarcinoma(274;0.0144)	5	771	-		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	248					A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	37	c.743G>A	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	C	5.496	0.276438	0.10403	.	.	ENSG00000137745	ENST00000260302;ENST00000546012;ENST00000340273	T;T	0.46819	0.86;0.86	5.59	4.68	0.58851	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.207964	0.52532	N	0.000079	T	0.16557	0.0398	N	0.01417	-0.88	0.44635	D	0.99761	B	0.02656	0.0	B	0.08055	0.003	T	0.20706	-1.0267	10	0.02654	T	1	.	10.717	0.46019	0.0:0.8549:0.0:0.1451	.	248	P45452	MMP13_HUMAN	D	248	ENSP00000260302:G248D;ENSP00000339672:G248D	ENSP00000260302:G248D	G	-	2	0	MMP13	102328007	0.817000	0.29147	1.000000	0.80357	0.983000	0.72400	1.516000	0.35856	1.479000	0.48272	0.655000	0.94253	GGC		0.448	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		4	197	0	0	0	1	0	4	197				
WDR44	54521	broad.mit.edu	37	X	117532360	117532360	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chrX:117532360G>A	ENST00000254029.3	+	8	1596	c.1201G>A	c.(1201-1203)Gca>Aca	p.A401T	WDR44_ENST00000371825.3_Missense_Mutation_p.A401T|WDR44_ENST00000371822.5_Missense_Mutation_p.A376T	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	401						endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						TAATGACGCGGCACAGTCAGA	0.363																																						ENST00000254029.3																			0				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						c.(1201-1203)Gca>Aca		WD repeat domain 44							134.0	115.0	122.0					X																	117532360		2203	4300	6503	SO:0001583	missense	54521					cytosol|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm		g.chrX:117532360G>A	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"""WD repeat domain containing"""	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.1201G>A	X.37:g.117532360G>A	ENSP00000254029:p.Ala401Thr					WDR44_ENST00000371825.3_Missense_Mutation_p.A401T|WDR44_ENST00000371822.5_Missense_Mutation_p.A376T	p.A401T	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN			8	1596	+			401					B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Missense_Mutation	SNP	ENST00000254029.3	37	c.1201G>A	CCDS14572.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.37|16.37	3.103918|3.103918	0.56291|0.56291	.|.	.|.	ENSG00000131725|ENSG00000131725	ENST00000371822;ENST00000254029;ENST00000371825|ENST00000371848	T;T;T|.	0.74209|.	-0.82;-0.22;-0.09|.	5.92|5.92	5.05|5.05	0.67936|0.67936	.|.	0.045243|.	0.85682|.	N|.	0.000000|.	T|T	0.52565|0.52565	0.1742|0.1742	L|L	0.29908|0.29908	0.895|0.895	0.47994|0.47994	D|D	0.999561|0.999561	B;B;B;B|.	0.16166|.	0.001;0.005;0.016;0.0|.	B;B;B;B|.	0.14578|.	0.004;0.008;0.011;0.003|.	T|T	0.47249|0.47249	-0.9132|-0.9132	10|5	0.14656|.	T|.	0.56|.	-31.2477|-31.2477	12.5547|12.5547	0.56246|0.56246	0.082:0.0:0.918:0.0|0.082:0.0:0.918:0.0	.|.	376;401;401;401|.	F8W913;E9PCI7;Q5JSH3-2;Q5JSH3|.	.;.;.;WDR44_HUMAN|.	T|D	376;401;401|300	ENSP00000360887:A376T;ENSP00000254029:A401T;ENSP00000360890:A401T|.	ENSP00000254029:A401T|.	A|G	+|+	1|2	0|0	WDR44|WDR44	117416388|117416388	1.000000|1.000000	0.71417|0.71417	0.887000|0.887000	0.34795|0.34795	0.910000|0.910000	0.53928|0.53928	7.697000|7.697000	0.84279|0.84279	1.229000|1.229000	0.43630|0.43630	0.600000|0.600000	0.82982|0.82982	GCA|GGC		0.363	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045		3	45	0	0	0	1	0	3	45				
TEX9	374618	broad.mit.edu	37	15	56680674	56680674	+	Missense_Mutation	SNP	C	C	G			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr15:56680674C>G	ENST00000352903.2	+	5	292	c.268C>G	c.(268-270)Ctg>Gtg	p.L90V	TEX9_ENST00000558083.2_Missense_Mutation_p.L15V|TEX9_ENST00000537232.1_Missense_Mutation_p.L15V|TEX9_ENST00000561221.2_Missense_Mutation_p.L90V	NM_198524.1	NP_940926.1	Q8N6V9	TEX9_HUMAN	testis expressed 9	90										cervix(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	14				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		CTGTAGAGGTCTGTTACCATC	0.308																																						ENST00000558083.2																			0				cervix(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	14						c.(43-45)Ctg>Gtg		testis expressed 9							101.0	101.0	101.0					15																	56680674		2193	4291	6484	SO:0001583	missense	374618							g.chr15:56680674C>G	BC028119	CCDS10157.1, CCDS66776.1	15q21.3	2007-03-13	2007-03-13		ENSG00000151575	ENSG00000151575			29585	protein-coding gene	gene with protein product			"""testis expressed sequence 9"""				Standard	XM_005254361		Approved		uc002adp.3	Q8N6V9	OTTHUMG00000132035	ENST00000352903.2:c.268C>G	15.37:g.56680674C>G	ENSP00000342169:p.Leu90Val					TEX9_ENST00000561221.2_Missense_Mutation_p.L90V|TEX9_ENST00000352903.2_Missense_Mutation_p.L90V|TEX9_ENST00000537232.1_Missense_Mutation_p.L15V	p.L15V			Q8N6V9	TEX9_HUMAN		all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)	4	373	+			90					B4DH73	Missense_Mutation	SNP	ENST00000352903.2	37	c.43C>G	CCDS10157.1	.	.	.	.	.	.	.	.	.	.	C	0.238	-1.015697	0.02078	.	.	ENSG00000151575	ENST00000352903;ENST00000537232	.	.	.	5.45	2.22	0.28083	.	1.167680	0.06118	N	0.668350	T	0.38772	0.1053	L	0.50333	1.59	0.09310	N	1	B;B	0.30973	0.277;0.302	B;B	0.33042	0.157;0.154	T	0.30592	-0.9973	9	0.29301	T	0.29	-1.5872	7.2647	0.26224	0.0:0.6634:0.138:0.1986	.	15;90	B4DH73;Q8N6V9	.;TEX9_HUMAN	V	90;15	.	ENSP00000342169:L90V	L	+	1	2	TEX9	54467966	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	0.140000	0.16056	0.087000	0.17167	-0.795000	0.03280	CTG		0.308	TEX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255048.2	NM_198524		17	110	0	0	0	1	0	17	110				
RPF1	80135	broad.mit.edu	37	1	84948626	84948626	+	Missense_Mutation	SNP	T	T	C			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr1:84948626T>C	ENST00000370654.5	+	3	329	c.314T>C	c.(313-315)aTt>aCt	p.I105T	RPF1_ENST00000370656.1_Missense_Mutation_p.I105T	NM_025065.6	NP_079341.2	Q9H9Y2	RPF1_HUMAN	ribosome production factor 1 homolog (S. cerevisiae)	105					rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						CCCAAGACCATTGACAACCAG	0.338																																						ENST00000370654.5																			0				breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						c.(313-315)aTt>aCt		ribosome production factor 1 homolog (S. cerevisiae)							110.0	102.0	105.0					1																	84948626		2203	4300	6503	SO:0001583	missense	80135				rRNA processing|translation	nucleolus	aminoacyl-tRNA ligase activity|ATP binding|rRNA binding	g.chr1:84948626T>C	AF322053	CCDS695.1	1p22.3	2009-09-25	2009-09-25	2009-09-25	ENSG00000117133	ENSG00000117133			30350	protein-coding gene	gene with protein product	"""RNA processing factor 1"", ""ribosome production factor 1"""		"""brix domain containing 5"""	BXDC5		11864606	Standard	NM_025065		Approved		uc001djv.4	Q9H9Y2	OTTHUMG00000009857	ENST00000370654.5:c.314T>C	1.37:g.84948626T>C	ENSP00000359688:p.Ile105Thr					RPF1_ENST00000370656.1_Missense_Mutation_p.I105T	p.I105T	NM_025065.6	NP_079341.2	Q9H9Y2	RPF1_HUMAN			3	329	+			105					Q5VSK7|Q6AHX1|Q8WXZ8	Missense_Mutation	SNP	ENST00000370654.5	37	c.314T>C	CCDS695.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.982954	0.74474	.	.	ENSG00000117133	ENST00000370656;ENST00000370654	T;T	0.64991	-0.13;1.27	5.93	5.93	0.95920	.	0.047740	0.85682	D	0.000000	T	0.82235	0.4993	H	0.94222	3.51	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.87546	0.2462	10	0.87932	D	0	-15.7871	16.3766	0.83401	0.0:0.0:0.0:1.0	.	105	Q9H9Y2	RPF1_HUMAN	T	105	ENSP00000359690:I105T;ENSP00000359688:I105T	ENSP00000359688:I105T	I	+	2	0	RPF1	84721214	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	7.236000	0.78154	2.263000	0.75096	0.533000	0.62120	ATT		0.338	RPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027238.1	NM_025065		3	38	0	0	0	1	0	3	38				
INTS4L2	644619	broad.mit.edu	37	7	65154327	65154327	+	RNA	SNP	T	T	C			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr7:65154327T>C	ENST00000430126.2	+	0	811							Q2T9F4	IN4L2_HUMAN	integrator complex subunit 4-like 2																		GCTGTACTAATGTTTCAACCA	0.363																																						ENST00000430126.2																			0																																																			0							g.chr7:65154327T>C	BC111554		7q11.21	2013-03-26			ENSG00000232270	ENSG00000273024			22351	other	unknown							Standard	NR_027392		Approved	MGC133166	uc003tue.2	Q2T9F4	OTTHUMG00000156558		7.37:g.65154327T>C														0	811	+									RNA	SNP	ENST00000430126.2	37																																																																																						0.363	INTS4L2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345545.2	NR_027392		4	42	0	0	0	1	0	4	42				
IKBKB	3551	broad.mit.edu	37	8	42171853	42171853	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr8:42171853C>T	ENST00000520810.1	+	9	892	c.706C>T	c.(706-708)Cgg>Tgg	p.R236W	IKBKB_ENST00000379708.3_Missense_Mutation_p.R13W|IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000520835.1_Missense_Mutation_p.R234W|IKBKB_ENST00000416505.2_Missense_Mutation_p.R177W	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	236	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	TTCAAAAGTGCGGCAGAAGAG	0.423																																						ENST00000520810.1																			0				breast(4)|lung(1)|ovary(2)|skin(1)	8						c.(706-708)Cgg>Tgg		inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	Arsenic trioxide(DB01169)|Auranofin(DB00995)						231.0	204.0	213.0					8																	42171853		2203	4300	6503	SO:0001583	missense	3551				anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity	g.chr8:42171853C>T	AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.706C>T	8.37:g.42171853C>T	ENSP00000430684:p.Arg236Trp					IKBKB_ENST00000520835.1_Missense_Mutation_p.R234W|IKBKB_ENST00000379708.3_Missense_Mutation_p.R13W|IKBKB_ENST00000416505.2_Missense_Mutation_p.R177W|IKBKB_ENST00000522147.1_Intron	p.R236W	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		9	892	+	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	236			Protein kinase.		B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	37	c.706C>T	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.804450	0.90623	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	T;T;T;T	0.43688	0.94;0.94;0.94;2.75	5.95	5.95	0.96441	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.053661	0.85682	D	0.000000	T	0.62660	0.2446	L	0.49350	1.555	0.58432	D	0.99999	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.977;0.931;0.998;0.959;0.959;0.927	T	0.61357	-0.7079	10	0.72032	D	0.01	.	20.3854	0.98941	0.0:1.0:0.0:0.0	.	177;234;13;187;236;236	B4E0U4;O14920-2;B3KRB7;Q59GL9;O14920;Q32ND9	.;.;.;.;IKKB_HUMAN;.	W	236;177;234;13	ENSP00000430684:R236W;ENSP00000404920:R177W;ENSP00000430868:R234W;ENSP00000369030:R13W	ENSP00000369030:R13W	R	+	1	2	IKBKB	42291010	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	5.693000	0.68264	2.825000	0.97269	0.655000	0.94253	CGG		0.423	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1			4	125	0	0	0	1	0	4	125				
TRUB1	142940	broad.mit.edu	37	10	116698112	116698112	+	Missense_Mutation	SNP	A	A	C	rs199739741		TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr10:116698112A>C	ENST00000298746.3	+	1	161	c.100A>C	c.(100-102)Acc>Ccc	p.T34P		NM_139169.4	NP_631908.1	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase family member 1	34					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.T34P(1)		breast(2)|kidney(2)|large_intestine(1)|lung(5)|urinary_tract(2)	12		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		AATGGCTGCGACCCCGTCAGC	0.637																																						ENST00000298746.3																			1	Substitution - Missense(1)	p.T34P(1)	kidney(1)	breast(2)|kidney(2)|large_intestine(1)|lung(5)|urinary_tract(2)	12						c.(100-102)Acc>Ccc		TruB pseudouridine (psi) synthase family member 1							10.0	12.0	11.0					10																	116698112		2149	4210	6359	SO:0001583	missense	142940				pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding	g.chr10:116698112A>C	AF448144	CCDS7591.1	10q25.3	2013-09-02	2013-09-02		ENSG00000165832	ENSG00000165832			16060	protein-coding gene	gene with protein product		610726	"""TruB pseudouridine (psi) synthase homolog 1 (E. coli)"""			12736709	Standard	NM_139169		Approved	PUS4	uc001lcd.3	Q8WWH5	OTTHUMG00000019094	ENST00000298746.3:c.100A>C	10.37:g.116698112A>C	ENSP00000298746:p.Thr34Pro						p.T34P	NM_139169.4	NP_631908.1	Q8WWH5	TRUB1_HUMAN		Epithelial(162;0.00879)|all cancers(201;0.0243)	1	161	+		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)	34					B2R716|Q53ES2	Missense_Mutation	SNP	ENST00000298746.3	37	c.100A>C	CCDS7591.1	.	.	.	.	.	.	.	.	.	.	A	16.81	3.226928	0.58668	.	.	ENSG00000165832	ENST00000298746	T	0.47528	0.84	5.36	-0.135	0.13477	.	1.208560	0.05856	N	0.622118	T	0.36580	0.0972	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36578	-0.9742	10	0.72032	D	0.01	0.0098	5.2826	0.15684	0.4598:0.1581:0.3821:0.0	.	34	Q8WWH5	TRUB1_HUMAN	P	34	ENSP00000298746:T34P	ENSP00000298746:T34P	T	+	1	0	TRUB1	116688102	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-0.006000	0.12833	0.023000	0.15187	-0.250000	0.11733	ACC		0.637	TRUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050504.1	NM_139169		5	7	0	0	0	1	0	5	7				
RP11-156P1.3	0	broad.mit.edu	37	17	45128792	45128792	+	RNA	SNP	G	G	T			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr17:45128792G>T	ENST00000575173.1	-	0	418				LRRC37A17P_ENST00000570478.1_RNA																							AATTCAGGTTGTCAGAATGCA	0.373																																						ENST00000575173.1																			0																																																			0							g.chr17:45128792G>T																													17.37:g.45128792G>T														0	418	-									RNA	SNP	ENST00000575173.1	37																																																																																						0.373	RP11-156P1.3-009	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000440924.1			4	73	1	0	0.00909568	1	0.00909568	4	73				
STAG1	10274	broad.mit.edu	37	3	136062803	136062803	+	Missense_Mutation	SNP	A	A	C			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr3:136062803A>C	ENST00000383202.2	-	30	3573	c.3317T>G	c.(3316-3318)aTt>aGt	p.I1106S	STAG1_ENST00000536929.1_Missense_Mutation_p.I690S|STAG1_ENST00000434713.2_Missense_Mutation_p.I846S|STAG1_ENST00000236698.5_Missense_Mutation_p.I1106S	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1106					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						AGGAGTCTGAATCATGGTGTC	0.507																																						ENST00000383202.2																			0				NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						c.(3316-3318)aTt>aGt		stromal antigen 1							143.0	117.0	126.0					3																	136062803		2203	4300	6503	SO:0001583	missense	10274				cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding	g.chr3:136062803A>C	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.3317T>G	3.37:g.136062803A>C	ENSP00000372689:p.Ile1106Ser					STAG1_ENST00000536929.1_Missense_Mutation_p.I690S|STAG1_ENST00000236698.5_Missense_Mutation_p.I1106S|STAG1_ENST00000434713.2_Missense_Mutation_p.I846S	p.I1106S	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN			30	3573	-			1106					O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	c.3317T>G	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.327459	0.60743	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.31769	1.89;1.88;1.86;1.48	5.48	5.48	0.80851	.	0.103074	0.41938	D	0.000789	T	0.24547	0.0595	L	0.40543	1.245	0.49582	D	0.999805	B;B	0.23650	0.089;0.003	B;B	0.15870	0.014;0.003	T	0.05954	-1.0854	10	0.14656	T	0.56	.	14.1559	0.65417	1.0:0.0:0.0:0.0	.	1106;1106	Q6P275;Q8WVM7	.;STAG1_HUMAN	S	1106;1106;846;690	ENSP00000372689:I1106S;ENSP00000236698:I1106S;ENSP00000404396:I846S;ENSP00000445787:I690S	ENSP00000236698:I1106S	I	-	2	0	STAG1	137545493	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.923000	0.92808	2.078000	0.62432	0.533000	0.62120	ATT		0.507	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		9	71	0	0	0	1	0	9	71				
LOC101927209	101927209	broad.mit.edu	37	1	142713773	142713773	+	lincRNA	SNP	C	C	G	rs199933143		TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr1:142713773C>G	ENST00000610091.1	-	0	1885																											TCTTTTTCCACATTGTCATTT	0.284																																						ENST00000369381.2																			0																																																			0							g.chr1:142713773C>G																													1.37:g.142713773C>G														0	832	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.284	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			5	101	0	0	0	1	0	5	101				
TDP1	55775	broad.mit.edu	37	14	90429610	90429610	+	Missense_Mutation	SNP	C	C	A			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr14:90429610C>A	ENST00000335725.4	+	3	402	c.152C>A	c.(151-153)gCc>gAc	p.A51D	TDP1_ENST00000555880.1_Missense_Mutation_p.A51D|TDP1_ENST00000393454.2_Missense_Mutation_p.A51D|TDP1_ENST00000393452.3_Missense_Mutation_p.A51D|TDP1_ENST00000555565.1_Intron|TDP1_ENST00000357382.3_5'UTR	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	51					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		TGTTCCGAGGCCCAGAAAGCT	0.488								Repair of DNA-protein crosslinks																														ENST00000335725.4																			0				NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25						c.(151-153)gCc>gAc	Repair of DNA-protein crosslinks	tyrosyl-DNA phosphodiesterase 1							112.0	106.0	108.0					14																	90429610		2203	4300	6503	SO:0001583	missense	55775				cell death|double-strand break repair|single strand break repair	cytoplasm|nucleus	3'-tyrosyl-DNA phosphodiesterase activity|double-stranded DNA binding|exonuclease activity|protein binding|single-stranded DNA binding	g.chr14:90429610C>A	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.152C>A	14.37:g.90429610C>A	ENSP00000337353:p.Ala51Asp					TDP1_ENST00000555565.1_Intron|TDP1_ENST00000393454.2_Missense_Mutation_p.A51D|TDP1_ENST00000357382.3_5'UTR|TDP1_ENST00000393452.3_Missense_Mutation_p.A51D|TDP1_ENST00000555880.1_Missense_Mutation_p.A51D	p.A51D	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN		COAD - Colon adenocarcinoma(157;0.23)	3	402	+		all_cancers(154;0.185)	51					Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	37	c.152C>A	CCDS9888.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.403879	0.83230	.	.	ENSG00000042088	ENST00000393452;ENST00000554180;ENST00000393454;ENST00000335725;ENST00000556867;ENST00000553527;ENST00000553989;ENST00000556498;ENST00000555880	T;T;T;T;T;T;T;T;T	0.40756	1.19;1.85;1.5;1.5;1.04;1.04;1.04;1.02;1.21	5.55	5.55	0.83447	.	0.050382	0.85682	D	0.000000	T	0.64918	0.2642	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.997;1.0;0.998	T	0.62581	-0.6824	10	0.42905	T	0.14	-22.6395	19.5117	0.95144	0.0:1.0:0.0:0.0	.	51;51;51;51	G3V2F4;E7EPD8;G3V4W8;Q9NUW8	.;.;.;TYDP1_HUMAN	D	51	ENSP00000377098:A51D;ENSP00000450872:A51D;ENSP00000377099:A51D;ENSP00000337353:A51D;ENSP00000452279:A51D;ENSP00000451358:A51D;ENSP00000452333:A51D;ENSP00000452183:A51D;ENSP00000450628:A51D	ENSP00000337353:A51D	A	+	2	0	TDP1	89499363	1.000000	0.71417	0.978000	0.43139	0.613000	0.37349	6.417000	0.73337	2.595000	0.87683	0.561000	0.74099	GCC		0.488	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		4	57	1	0	2.56e-06	1	2.67636e-06	4	57				
OLFML2B	25903	broad.mit.edu	37	1	161967655	161967655	+	Silent	SNP	C	C	T			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr1:161967655C>T	ENST00000294794.3	-	6	1857	c.1434G>A	c.(1432-1434)acG>acA	p.T478T	OLFML2B_ENST00000367940.2_Silent_p.T479T	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	478					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			CGGGGCTCAGCGTGGGGCTGG	0.562																																						ENST00000294794.3																			0				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						c.(1432-1434)acG>acA		olfactomedin-like 2B							143.0	143.0	143.0					1																	161967655		2203	4300	6503	SO:0001819	synonymous_variant	25903							g.chr1:161967655C>T	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.1434G>A	1.37:g.161967655C>T						OLFML2B_ENST00000367940.2_Silent_p.T479T	p.T478T	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.0172)		6	1857	-	all_hematologic(112;0.156)		478					B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Silent	SNP	ENST00000294794.3	37	c.1434G>A	CCDS1236.1																																																																																				0.562	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		13	195	0	0	0	1	0	13	195				
MYPOP	339344	broad.mit.edu	37	19	46393884	46393884	+	Silent	SNP	C	C	T			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr19:46393884C>T	ENST00000322217.5	-	3	1283	c.1197G>A	c.(1195-1197)ccG>ccA	p.P399P		NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	399						nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						GTAGATTTCACGGAGATTTCC	0.642																																						ENST00000322217.5																			0				large_intestine(2)|lung(1)|skin(1)	4						c.(1195-1197)ccG>ccA		Myb-related transcription factor, partner of profilin							36.0	39.0	38.0					19																	46393884		2091	4209	6300	SO:0001819	synonymous_variant	339344					nucleus	DNA binding	g.chr19:46393884C>T	BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182			20178	protein-coding gene	gene with protein product	"""p42 Myb-related transcription factor, partner of profilin"""					15615774	Standard	NM_001012643		Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.1197G>A	19.37:g.46393884C>T							p.P399P	NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN			3	1283	-			399						Silent	SNP	ENST00000322217.5	37	c.1197G>A	CCDS33055.1																																																																																				0.642	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461684.1	NM_001012643		3	43	0	0	0	1	0	3	43				
ADCY6	112	broad.mit.edu	37	12	49170258	49170258	+	Silent	SNP	G	G	A			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr12:49170258G>A	ENST00000307885.4	-	6	2182	c.1488C>T	c.(1486-1488)tcC>tcT	p.S496S	ADCY6_ENST00000550422.1_Silent_p.S496S|ADCY6_ENST00000552090.1_5'UTR|ADCY6_ENST00000357869.3_Silent_p.S496S	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	496					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						TCACATCATTGGACCACACAT	0.647																																						ENST00000307885.4																			0				breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						c.(1486-1488)tcC>tcT		adenylate cyclase 6							69.0	61.0	64.0					12																	49170258		2203	4299	6502	SO:0001819	synonymous_variant	112				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane	ATP binding|metal ion binding	g.chr12:49170258G>A		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"""Adenylate cyclases"""	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.1488C>T	12.37:g.49170258G>A						ADCY6_ENST00000552090.1_5'UTR|ADCY6_ENST00000357869.3_Silent_p.S496S|ADCY6_ENST00000550422.1_Silent_p.S496S	p.S496S	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN			6	2182	-			496					Q9NR75|Q9UDB0	Silent	SNP	ENST00000307885.4	37	c.1488C>T	CCDS8767.1																																																																																				0.647	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983		5	36	0	0	0	1	0	5	36				
SLC26A5	375611	broad.mit.edu	37	7	103017289	103017289	+	Silent	SNP	G	G	A			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr7:103017289G>A	ENST00000306312.3	-	19	2268	c.2007C>T	c.(2005-2007)gaC>gaT	p.D669D	SLC26A5_ENST00000393723.1_Silent_p.D639D|SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000393727.1_Silent_p.D671D|SLC26A5_ENST00000356767.4_Intron|SLC26A5_ENST00000354356.4_Silent_p.D102D|SLC26A5_ENST00000393730.1_Silent_p.D637D|SLC26A5_ENST00000393729.1_Silent_p.D632D|SLC26A5_ENST00000432958.2_Silent_p.D637D|SLC26A5_ENST00000339444.6_Silent_p.D669D	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	669	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						ATATACCGACGTCTCCATATT	0.308																																						ENST00000306312.3																			0				endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						c.(2005-2007)gaC>gaT		solute carrier family 26 (anion exchanger), member 5							110.0	113.0	112.0					7																	103017289		2203	4295	6498	SO:0001819	synonymous_variant	375611				regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity	g.chr7:103017289G>A	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"""Solute carriers"""	9359	protein-coding gene	gene with protein product	"""deafness, neurosensory, autosomal recessive, 61"""	604943	"""prestin (motor protein)"""	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.2007C>T	7.37:g.103017289G>A						SLC26A5_ENST00000339444.6_Silent_p.D669D|SLC26A5_ENST00000432958.2_Silent_p.D637D|SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000393727.1_Silent_p.D671D|SLC26A5_ENST00000393730.1_Silent_p.D637D|SLC26A5_ENST00000393723.1_Silent_p.D639D|SLC26A5_ENST00000393729.1_Silent_p.D632D|SLC26A5_ENST00000354356.4_Silent_p.D102D|SLC26A5_ENST00000356767.4_Intron	p.D669D	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN			19	2268	-			669			STAS.		Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Silent	SNP	ENST00000306312.3	37	c.2007C>T	CCDS5733.1																																																																																				0.308	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		4	108	0	0	0	1	0	4	108				
FANK1	92565	broad.mit.edu	37	10	127693527	127693527	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr10:127693527C>T	ENST00000368693.1	+	7	718	c.614C>T	c.(613-615)gCt>gTt	p.A205V	FANK1_ENST00000477963.1_3'UTR|FANK1_ENST00000368695.1_Missense_Mutation_p.A199V			Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	205						cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				TCTTGGCAGGCTAGAGACCTG	0.532																																						ENST00000368695.1																			0				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21						c.(595-597)gCt>gTt		fibronectin type III and ankyrin repeat domains 1							165.0	157.0	160.0					10																	127693527		2203	4300	6503	SO:0001583	missense	92565					cytoplasm|nucleus		g.chr10:127693527C>T	BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	23527	protein-coding gene	gene with protein product		611640	"""fibronectin type 3 and ankyrin repeat domains 1"""			12477932	Standard	NM_145235		Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368693.1:c.614C>T	10.37:g.127693527C>T	ENSP00000357682:p.Ala205Val					FANK1_ENST00000477963.1_3'UTR|FANK1_ENST00000368693.1_Missense_Mutation_p.A205V	p.A199V	NM_145235.3	NP_660278.3	Q8TC84	FANK1_HUMAN			7	718	+		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)	205					Q6UXY9|Q6X7T6	Missense_Mutation	SNP	ENST00000368693.1	37	c.596C>T	CCDS31309.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.270434	0.40194	.	.	ENSG00000203780	ENST00000368695;ENST00000368693;ENST00000368691;ENST00000368692	T;T;T	0.67865	-0.08;-0.08;-0.29	5.79	4.87	0.63330	Ankyrin repeat-containing domain (4);	0.637984	0.15190	N	0.275622	T	0.65626	0.2709	L	0.46567	1.45	0.26941	N	0.966244	P;B;B	0.40083	0.702;0.421;0.338	B;B;B	0.43990	0.438;0.254;0.239	T	0.57665	-0.7772	10	0.33940	T	0.23	-8.4495	14.0992	0.65044	0.0:0.7128:0.2872:0.0	.	231;205;205	Q8TC84-3;Q8TC84-2;Q8TC84	.;.;FANK1_HUMAN	V	199;205;183;231	ENSP00000357684:A199V;ENSP00000357682:A205V;ENSP00000357680:A183V	ENSP00000357680:A183V	A	+	2	0	FANK1	127683517	0.004000	0.15560	0.015000	0.15790	0.587000	0.36485	1.833000	0.39161	1.408000	0.46895	0.655000	0.94253	GCT		0.532	FANK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145235		8	92	0	0	0	1	0	8	92				
TLE1	7088	broad.mit.edu	37	9	84202651	84202651	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr9:84202651C>T	ENST00000376499.3	-	17	2986	c.1922G>A	c.(1921-1923)aGg>aAg	p.R641K		NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	641					multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						GTCCCAGGACCTGACTGTGTT	0.597																																					NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	ENST00000376499.3																			0				NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						c.(1921-1923)aGg>aAg		transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)							66.0	64.0	65.0					9																	84202651		2203	4300	6503	SO:0001583	missense	7088				negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding	g.chr9:84202651C>T		CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781		"""WD repeat domain containing"""	11837	protein-coding gene	gene with protein product	"""enhancer of split groucho 1"""	600189	"""transducin-like enhancer of split 1, homolog of Drosophila E(sp1)"""			8365415, 8808280	Standard	NM_005077		Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.1922G>A	9.37:g.84202651C>T	ENSP00000365682:p.Arg641Lys						p.R641K	NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN			17	2986	-			641					A8K495|Q5T3G4|Q969V9	Missense_Mutation	SNP	ENST00000376499.3	37	c.1922G>A	CCDS6661.1	.	.	.	.	.	.	.	.	.	.	c	37	6.133791	0.97315	.	.	ENSG00000196781	ENST00000376499	T	0.60548	0.18	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.71204	0.3312	L	0.39147	1.195	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.999	T	0.72447	-0.4291	10	0.87932	D	0	-19.5912	19.9738	0.97296	0.0:1.0:0.0:0.0	.	626;641	B4DEF9;Q04724	.;TLE1_HUMAN	K	641	ENSP00000365682:R641K	ENSP00000365682:R641K	R	-	2	0	TLE1	83392471	1.000000	0.71417	0.981000	0.43875	0.997000	0.91878	7.818000	0.86416	2.732000	0.93576	0.655000	0.94253	AGG		0.597	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077		5	62	0	0	0	1	0	5	62				
TUBBP5	643224	broad.mit.edu	37	9	141070139	141070139	+	RNA	SNP	C	C	T	rs143443709		TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr9:141070139C>T	ENST00000503395.1	+	0	1219									tubulin, beta pseudogene 5									p.L85F(2)									CGGGCAGGTCCTCAGGCCAGA	0.667																																						ENST00000503395.1																			2	Substitution - Missense(2)	p.L85F(2)	urinary_tract(1)|prostate(1)																																																0							g.chr9:141070139C>T	AF355123		9q34.3	2012-03-06	2005-11-15		ENSG00000159247	ENSG00000159247			23674	pseudogene	pseudogene			"""tubulin, beta polypeptide pseudogene 5"""			11731935	Standard	NR_027156		Approved		uc010ncq.3		OTTHUMG00000021001		9.37:g.141070139C>T														0	1219	+									RNA	SNP	ENST00000503395.1	37																																																																																						0.667	TUBBP5-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373087.1	NR_027156		4	62	0	0	0	1	0	4	62				
OR4C6	219432	broad.mit.edu	37	11	55432865	55432865	+	Missense_Mutation	SNP	G	G	A	rs201388016	byFrequency	TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr11:55432865G>A	ENST00000314259.3	+	1	252	c.223G>A	c.(223-225)Gtt>Att	p.V75I		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	75						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						CTCATCTGTCGTTGCCCCCAA	0.448													g|||	9	0.00179712	0.0008	0.0	5008	,	,		19397	0.002		0.001	False		,,,				2504	0.0051					ENST00000314259.3																			0				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						c.(223-225)Gtt>Att		olfactory receptor, family 4, subfamily C, member 6		G	ILE/VAL	1,4399	2.1+/-5.4	0,1,2199	248.0	215.0	226.0		223	-2.1	0.0	11		226	3,8589	3.0+/-9.4	0,3,4293	yes	missense	OR4C6	NM_001004704.1	29	0,4,6492	AA,AG,GG		0.0349,0.0227,0.0308	benign	75/310	55432865	4,12988	2200	4296	6496	SO:0001583	missense	219432				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55432865G>A	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"""GPCR / Class A : Olfactory receptors"""	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.223G>A	11.37:g.55432865G>A	ENSP00000324769:p.Val75Ile						p.V75I	NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN			1	252	+			75					B2RP11|Q6IFD2	Missense_Mutation	SNP	ENST00000314259.3	37	c.223G>A	CCDS31506.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	0.018	-1.476546	0.01035	2.27E-4	3.49E-4	ENSG00000181903	ENST00000314259	T	0.01406	4.93	3.83	-2.14	0.07123	GPCR, rhodopsin-like superfamily (1);	0.395490	0.18367	N	0.143383	T	0.00608	0.0020	N	0.05177	-0.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47774	-0.9091	10	0.02654	T	1	.	5.3444	0.16000	0.5373:0.149:0.3137:0.0	.	75	Q8NH72	OR4C6_HUMAN	I	75	ENSP00000324769:V75I	ENSP00000324769:V75I	V	+	1	0	OR4C6	55189441	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	0.095000	0.15127	-0.002000	0.14469	-1.261000	0.01458	GTT		0.448	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704		7	118	0	0	0	1	0	7	118				
TMPRSS15	5651	broad.mit.edu	37	21	19666747	19666747	+	Missense_Mutation	SNP	G	G	C			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr21:19666747G>C	ENST00000284885.3	-	21	2359	c.2326C>G	c.(2326-2328)Ctg>Gtg	p.L776V		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	776						brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TGAGCTGCCAGTTTTTTTCCA	0.423																																						ENST00000284885.3																			0				NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						c.(2326-2328)Ctg>Gtg		transmembrane protease, serine 15							89.0	99.0	95.0					21																	19666747		2203	4300	6503	SO:0001583	missense	5651				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity	g.chr21:19666747G>C		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.2326C>G	21.37:g.19666747G>C	ENSP00000284885:p.Leu776Val						p.L776V	NM_002772.2	NP_002763.2	P98073	ENTK_HUMAN			21	2359	-			776					Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	c.2326C>G	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	G	7.568	0.666088	0.14710	.	.	ENSG00000154646	ENST00000284885	D	0.86366	-2.11	5.94	-2.21	0.06973	Speract/scavenger receptor (1);Peptidase cysteine/serine, trypsin-like (1);Speract/scavenger receptor-related (1);	0.960292	0.08618	N	0.918913	D	0.82375	0.5023	L	0.56769	1.78	0.09310	N	1	P	0.35174	0.488	B	0.37731	0.257	T	0.69639	-0.5091	9	.	.	.	.	5.4482	0.16548	0.2065:0.0:0.3088:0.4846	.	776	P98073	ENTK_HUMAN	V	776	ENSP00000284885:L776V	.	L	-	1	2	TMPRSS15	18588618	0.003000	0.15002	0.000000	0.03702	0.571000	0.35966	-0.093000	0.11111	-0.405000	0.07599	-0.294000	0.09567	CTG		0.423	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		10	121	0	0	0	1	0	10	121				
NCAPD3	23310	broad.mit.edu	37	11	134029950	134029950	+	Missense_Mutation	SNP	C	C	T	rs375438498		TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr11:134029950C>T	ENST00000534548.2	-	29	3768	c.3704G>A	c.(3703-3705)cGa>cAa	p.R1235Q		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	1235					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		GAGCTCATCTCGGTAATCCTG	0.488																																						ENST00000534548.2																			0				NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						c.(3703-3705)cGa>cAa		non-SMC condensin II complex, subunit D3		C	GLN/ARG	0,4402		0,0,2201	118.0	107.0	111.0		3704	3.5	0.8	11		111	1,8593	1.2+/-3.3	0,1,4296	no	missense	NCAPD3	NM_015261.2	43	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	1235/1499	134029950	1,12995	2201	4297	6498	SO:0001583	missense	23310				cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding	g.chr11:134029950C>T	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.3704G>A	11.37:g.134029950C>T	ENSP00000433681:p.Arg1235Gln						p.R1235Q	NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)	29	3768	-	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)	1235					A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	c.3704G>A	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.376419	0.61735	0.0	1.16E-4	ENSG00000151503	ENST00000534548;ENST00000527944	T;T	0.65549	-0.16;-0.16	5.36	3.5	0.40072	Armadillo-type fold (1);	0.181068	0.48767	N	0.000162	T	0.48857	0.1523	L	0.47716	1.5	0.80722	D	1	P;P	0.35793	0.51;0.521	B;B	0.24541	0.046;0.054	T	0.50355	-0.8838	10	0.66056	D	0.02	-5.4033	10.1003	0.42499	0.0:0.7847:0.0:0.2153	.	1235;295	P42695;Q96FA6	CNDD3_HUMAN;.	Q	1235;140	ENSP00000433681:R1235Q;ENSP00000432532:R140Q	ENSP00000432532:R140Q	R	-	2	0	NCAPD3	133535160	0.996000	0.38824	0.799000	0.32177	0.983000	0.72400	3.324000	0.52022	0.750000	0.32877	0.655000	0.94253	CGA		0.488	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		10	73	0	0	0	1	0	10	73				
RP11-156P1.3	0	broad.mit.edu	37	17	45128812	45128812	+	RNA	SNP	C	C	T			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr17:45128812C>T	ENST00000575173.1	-	0	418				LRRC37A17P_ENST00000570478.1_RNA																							AGTCCTGTTTCTGTGTGGATT	0.373																																						ENST00000575173.1																			0																																																			0							g.chr17:45128812C>T																													17.37:g.45128812C>T														0	418	-									RNA	SNP	ENST00000575173.1	37																																																																																						0.373	RP11-156P1.3-009	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000440924.1			3	48	0	0	0	1	0	3	48				
AKR1B15	441282	broad.mit.edu	37	7	134252993	134252993	+	Silent	SNP	G	G	A			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr7:134252993G>A	ENST00000457545.2	+	4	494	c.234G>A	c.(232-234)gaG>gaA	p.E78E	AKR1B15_ENST00000423958.1_Silent_p.E50E	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	78							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						ATTTCTATGAGAATCAACATG	0.478																																						ENST00000457545.2																			0				endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						c.(232-234)gaG>gaA		aldo-keto reductase family 1, member B15							125.0	130.0	128.0					7																	134252993		2203	4300	6503	SO:0001819	synonymous_variant	441282						oxidoreductase activity	g.chr7:134252993G>A		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"""Aldo-keto reductases"""	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.234G>A	7.37:g.134252993G>A						AKR1B15_ENST00000423958.1_Silent_p.E50E	p.E78E	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN			4	494	+			78					C9J3V2	Silent	SNP	ENST00000457545.2	37	c.234G>A	CCDS47715.2																																																																																				0.478	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2			12	89	0	0	0	1	0	12	89				
ARPP21	10777	broad.mit.edu	37	3	35770839	35770839	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr3:35770839C>T	ENST00000187397.4	+	15	1726	c.1270C>T	c.(1270-1272)Cgc>Tgc	p.R424C	ARPP21_ENST00000337271.5_Missense_Mutation_p.R370C|ARPP21_ENST00000444190.1_Missense_Mutation_p.R370C|ARPP21_ENST00000458225.1_Missense_Mutation_p.R390C|ARPP21_ENST00000417925.1_Missense_Mutation_p.R390C	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	424					cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						ATCGCTGTCCCGCACCCATCC	0.552																																						ENST00000187397.4																			0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						c.(1270-1272)Cgc>Tgc		cAMP-regulated phosphoprotein, 21kDa							63.0	65.0	65.0					3																	35770839		2203	4300	6503	SO:0001583	missense	10777					cytoplasm	nucleic acid binding	g.chr3:35770839C>T	AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"""R3H domain containing 3"""	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.1270C>T	3.37:g.35770839C>T	ENSP00000187397:p.Arg424Cys					ARPP21_ENST00000458225.1_Missense_Mutation_p.R390C|ARPP21_ENST00000444190.1_Missense_Mutation_p.R370C|ARPP21_ENST00000337271.5_Missense_Mutation_p.R370C|ARPP21_ENST00000417925.1_Missense_Mutation_p.R390C	p.R424C	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN			15	1726	+			424					B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	37	c.1270C>T	CCDS2661.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.105000|5.105000	0.94245|0.94245	.|.	.|.	ENSG00000172995|ENSG00000172995	ENST00000425289|ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925	.|T;T;T;T;T	.|0.44083	.|0.93;0.93;0.93;0.93;0.93	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	.|0.739270	.|0.13443	.|N	.|0.387461	T|T	0.67439|0.67439	0.2893|0.2893	M|M	0.71036|0.71036	2.16|2.16	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.81914	.|0.995;0.989;0.993	T|T	0.60342|0.60342	-0.7282|-0.7282	5|10	.|0.39692	.|T	.|0.17	-13.081|-13.081	20.6397|20.6397	0.99537|0.99537	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|390;424;370	.|Q9UBL0-3;Q9UBL0;Q9UBL0-4	.|.;ARP21_HUMAN;.	L|C	196|390;370;370;424;390	.|ENSP00000414351:R390C;ENSP00000337792:R370C;ENSP00000405276:R370C;ENSP00000187397:R424C;ENSP00000412326:R390C	.|ENSP00000187397:R424C	P|R	+|+	2|1	0|0	ARPP21|ARPP21	35745843|35745843	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.989000|0.989000	0.77384|0.77384	4.678000|4.678000	0.61641|0.61641	2.880000|2.880000	0.98712|0.98712	0.650000|0.650000	0.86243|0.86243	CCG|CGC		0.552	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		3	44	0	0	0	1	0	3	44				
FAM135B	51059	broad.mit.edu	37	8	139263143	139263143	+	Silent	SNP	C	C	A			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr8:139263143C>A	ENST00000395297.1	-	6	653	c.483G>T	c.(481-483)ctG>ctT	p.L161L		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	161								p.L161L(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			AGATCACAGACAGGTGGAAAT	0.597										HNSCC(54;0.14)																												ENST00000395297.1																			2	Substitution - coding silent(2)	p.L161L(2)	lung(2)	NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238						c.(481-483)ctG>ctT		family with sequence similarity 135, member B							119.0	128.0	125.0					8																	139263143		2066	4207	6273	SO:0001819	synonymous_variant	51059							g.chr8:139263143C>A	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.483G>T	8.37:g.139263143C>A		HNSCC(54;0.14)					p.L161L	NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.0805)		6	653	-	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		161					B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	c.483G>T	CCDS6375.2																																																																																				0.597	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		19	87	1	0	2.35188e-11	1	2.51597e-11	19	87				
LAMA4	3910	broad.mit.edu	37	6	112430676	112430676	+	Silent	SNP	G	G	A			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr6:112430676G>A	ENST00000230538.7	-	39	5833	c.5436C>T	c.(5434-5436)agC>agT	p.S1812S	LAMA4_ENST00000522006.1_Silent_p.S1805S|LAMA4_ENST00000389463.4_Silent_p.S1805S|LAMA4_ENST00000424408.2_Silent_p.S1805S	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1812	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TTACGGCGCCGCTGACCAGGG	0.532																																						ENST00000230538.7																			0				NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100						c.(5434-5436)agC>agT		laminin, alpha 4							81.0	74.0	76.0					6																	112430676		2203	4300	6503	SO:0001819	synonymous_variant	3910				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding	g.chr6:112430676G>A		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.5436C>T	6.37:g.112430676G>A						LAMA4_ENST00000389463.4_Silent_p.S1805S|LAMA4_ENST00000424408.2_Silent_p.S1805S|LAMA4_ENST00000522006.1_Silent_p.S1805S	p.S1812S	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)	39	5833	-		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)	1812			Laminin G-like 5.		Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	c.5436C>T	CCDS43491.1																																																																																				0.532	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		3	52	0	0	0	1	0	3	52				
MAP1A	4130	broad.mit.edu	37	15	43816202	43816202	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr15:43816202C>T	ENST00000300231.5	+	4	2981	c.2531C>T	c.(2530-2532)tCa>tTa	p.S844L	MAP1A_ENST00000399453.1_Missense_Mutation_p.S844L|MAP1A_ENST00000382031.1_Missense_Mutation_p.S1082L			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	844					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TTTGCCACATCAGTGGCTGAG	0.532																																						ENST00000382031.1																			0				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66						c.(3244-3246)tCa>tTa		microtubule-associated protein 1A	Estramustine(DB01196)						55.0	54.0	54.0					15																	43816202		1979	4172	6151	SO:0001583	missense	4130					cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity	g.chr15:43816202C>T	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.2531C>T	15.37:g.43816202C>T	ENSP00000300231:p.Ser844Leu					MAP1A_ENST00000399453.1_Missense_Mutation_p.S844L|MAP1A_ENST00000300231.5_Missense_Mutation_p.S844L	p.S1082L			P78559	MAP1A_HUMAN		GBM - Glioblastoma multiforme(94;3.05e-06)	5	3276	+		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)	844					O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	c.3245C>T	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.238307	0.58886	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.56776	0.44;0.44;0.44	4.98	4.98	0.66077	.	.	.	.	.	T	0.73946	0.3652	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75693	-0.3229	9	0.51188	T	0.08	-10.2277	18.4428	0.90673	0.0:1.0:0.0:0.0	.	844	P78559	MAP1A_HUMAN	L	1082;844;844	ENSP00000371462:S1082L;ENSP00000382380:S844L;ENSP00000300231:S844L	ENSP00000300231:S844L	S	+	2	0	MAP1A	41603494	1.000000	0.71417	0.816000	0.32577	0.997000	0.91878	7.165000	0.77544	2.582000	0.87167	0.655000	0.94253	TCA		0.532	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		5	37	0	0	0	1	0	5	37				
IGHV4-59	28392	broad.mit.edu	37	14	107083278	107083278	+	RNA	SNP	G	G	A			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr14:107083278G>A	ENST00000455737.1	-	0	365									immunoglobulin heavy variable 4-59																		ATACACGGCCGTGTCCGCAGC	0.587																																						ENST00000455737.1																			0																				83.0	83.0	83.0					14																	107083278		1851	4084	5935			0							g.chr14:107083278G>A	L10088		14q32.33	2012-02-08			ENSG00000224373	ENSG00000224373		"""Immunoglobulins / IGH locus"""	5654	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151973		14.37:g.107083278G>A														0	365	-									RNA	SNP	ENST00000455737.1	37																																																																																						0.587	IGHV4-59-002	KNOWN	basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000324620.1	NG_001019		4	226	0	0	0	1	0	4	226				
WASH3P	374666	broad.mit.edu	37	15	102516473	102516473	+	RNA	SNP	G	G	A			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr15:102516473G>A	ENST00000557932.1	+	0	1421				DDX11L9_ENST00000562189.1_RNA			C4AMC7	WASH3_HUMAN	WAS protein family homolog 3 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)			central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						ATCCTAGGGGGCTCCATGACA	0.642																																						ENST00000557932.1																			0				central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25																																														0							g.chr15:102516473G>A			15q26.3	2014-03-20	2008-01-16	2008-01-16	ENSG00000185596	ENSG00000185596		"""WAS protein homologs"""	24362	pseudogene	pseudogene			"""family with sequence similarity 39, member D pseudogene"""	FAM39DP		11701968, 18159949	Standard	NR_003659		Approved	FLJ25222	uc002cdi.3	C4AMC7	OTTHUMG00000172275		15.37:g.102516473G>A														0	1421	+									RNA	SNP	ENST00000557932.1	37																																																																																						0.642	WASH3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417608.1	NM_199163		4	68	0	0	0	1	0	4	68				
LOC101927209	101927209	broad.mit.edu	37	1	142713774	142713774	+	lincRNA	SNP	A	A	G	rs201023195		TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr1:142713774A>G	ENST00000610091.1	-	0	1884																											CTTTTTCCACATTGTCATTTT	0.284																																						ENST00000369381.2																			0																																																			0							g.chr1:142713774A>G																													1.37:g.142713774A>G														0	831	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.284	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			5	102	0	0	0	1	0	5	102				
KRT16	3868	broad.mit.edu	37	17	39767650	39767650	+	Nonsense_Mutation	SNP	G	G	A			TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr17:39767650G>A	ENST00000301653.4	-	3	782	c.718C>T	c.(718-720)Cag>Tag	p.Q240*		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	240	Coil 1B.|Rod.				aging (GO:0007568)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|epidermis development (GO:0008544)|hair cycle (GO:0042633)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of cell migration (GO:0030336)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Breast(137;0.000307)				CCTTCGATCTGCATCTCCAGG	0.637																																						ENST00000301653.4																			0				NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						c.(718-720)Cag>Tag		keratin 16							79.0	77.0	78.0					17																	39767650		2203	4300	6503	SO:0001587	stop_gained	3868				cell proliferation|epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton	g.chr17:39767650G>A	S79867	CCDS11401.1	17q21.2	2013-01-16	2008-08-01		ENSG00000186832	ENSG00000186832		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6423	protein-coding gene	gene with protein product	"""focal non-epidermolytic palmoplantar keratoderma"""	148067				2451124, 16831889	Standard	NM_005557		Approved	NEPPK	uc002hxg.4	P08779	OTTHUMG00000133495	ENST00000301653.4:c.718C>T	17.37:g.39767650G>A	ENSP00000301653:p.Gln240*						p.Q240*	NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN			3	782	-		Breast(137;0.000307)	240			Coil 1B.|Rod.		A8K488|P30654|Q16402|Q9UBG8	Nonsense_Mutation	SNP	ENST00000301653.4	37	c.718C>T	CCDS11401.1	.	.	.	.	.	.	.	.	.	.	G	36	5.737198	0.96865	.	.	ENSG00000186832	ENST00000301653	.	.	.	4.63	4.63	0.57726	.	0.000000	0.48767	D	0.000170	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.0402	0.89317	0.0:0.0:1.0:0.0	.	.	.	.	X	240	.	ENSP00000301653:Q240X	Q	-	1	0	KRT16	37021176	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	5.409000	0.66374	2.556000	0.86216	0.561000	0.74099	CAG		0.637	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557		13	98	0	0	0	1	0	13	98				
RP5-884C9.2	0	broad.mit.edu	37	1	38546374	38546377	+	lincRNA	DEL	CTTA	CTTA	-	rs577750671	byFrequency	TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr1:38546374_38546377delCTTA	ENST00000432922.1	+	0	301																											CTTTGAAAGGCTTACTTTCAAAAC	0.363														9	0.00179712	0.0	0.0014	5008	,	,		21009	0.0		0.008	False		,,,				2504	0.0					ENST00000432922.1																			0																																																			0							g.chr1:38546374_38546377delCTTA																													1.37:g.38546374_38546377delCTTA														0	301	+									RNA	DEL	ENST00000432922.1	37																																																																																						0.363	RP5-884C9.2-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000001201.1			3	4						3	4	---	---	---	---
IGHJ6	28475	broad.mit.edu	37	14	106329450	106329451	+	RNA	INS	-	-	ACC	rs2338628|rs67183528|rs376479093|rs74454466	byFrequency	TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr14:106329450_106329451insACC	ENST00000390560.2	-	0	17_18				IGHJ5_ENST00000488476.1_RNA|IGHJ2_ENST00000390564.2_RNA|IGHD7-27_ENST00000439842.1_RNA|IGHJ4_ENST00000461719.1_RNA|IGHJ3_ENST00000463911.1_RNA|IGHJ1_ENST00000390565.1_RNA					immunoglobulin heavy joining 6																		CAGACGTCCATGTAGTAGTAGT	0.54																																						ENST00000390560.2																			0																																																			0							g.chr14:106329450_106329451insACC	J00256		14q32.33	2012-02-08			ENSG00000211900	ENSG00000211900		"""Immunoglobulins / IGH locus"""	5540	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152455		14.37:g.106329450_106329451insACC														0	17_18	-									RNA	INS	ENST00000390560.2	37																																																																																						0.540	IGHJ6-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_start_NF|cds_end_NF|basic|appris_principal	IG_J_gene	IG_J_gene	OTTHUMT00000326277.1	NG_001019		7	92						7	92	---	---	---	---
TBC1D3P2	440452	broad.mit.edu	37	17	60347260	60347260	+	IGR	DEL	T	T	-	rs548240589	byFrequency	TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr17:60347260delT	ENST00000602932.1	-	0	397				TBC1D3P2_ENST00000581291.1_RNA																							CTCTGAATGATTTTTTTTTTT	0.448													|||unknown(NO_COVERAGE)	1228	0.245208	0.1778	0.2882	5008	,	,		28738	0.1518		0.3688	False		,,,				2504	0.2751					ENST00000581291.1																			0				breast(2)|kidney(1)|lung(2)	5																																												SO:0001628	intergenic_variant	0							g.chr17:60347260delT																													17.37:g.60347260delT														0	581	-									RNA	DEL	ENST00000602932.1	37																																																																																						0.448	RP11-51L5.7-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000467667.1			4	8						4	8	---	---	---	---
ANKRD20A11P	391267	broad.mit.edu	37	21	15347257	15347258	+	RNA	INS	-	-	A	rs80199214		TCGA-KK-A8I7-01A-21D-A364-08	TCGA-KK-A8I7-11A-12D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ad18700a-4894-4c51-9d92-68514c853b0c	7e2e1f2f-9929-485e-8b8f-cb092a7e3b1c	g.chr21:15347257_15347258insA	ENST00000344693.5	-	0	736					NR_027270.1				ankyrin repeat domain 20 family, member A11, pseudogene																		ACCCTGCACAGAAAAAAAGTTG	0.307																																						ENST00000344693.5																			0																																																			0							g.chr21:15347257_15347258insA			21q11.2	2011-11-23			ENSG00000215559	ENSG00000215559			42024	pseudogene	pseudogene			"""chromosome 21 open reading frame 81"""	C21orf81			Standard	NR_027270		Approved		uc002yjj.4		OTTHUMG00000074237		21.37:g.15347264_15347264dupA								NR_027270.1						0	736	-									RNA	INS	ENST00000344693.5	37																																																																																						0.307	ANKRD20A11P-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157750.1			4	7						4	7	---	---	---	---
