#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov	i_TVarCov	i_Transcript_Id	i_Trna_alt1	i_Trna_alt2	i_Trna_ref	i_Trna_tot	i_Trna_var	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	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
FAM132A	388581	ucsc.edu	37	1	1179654	1179654	+	Splice_Site	SNP	C	C	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr1:1179654C>A	ENST00000330388.2	-	3	327	c.296G>T	c.(295-297)cGg>cTg	p.R99L		NM_001014980.2	NP_001014980.1	Q5T7M4	ADIPL_HUMAN	family with sequence similarity 132, member A	99					negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of glucose import (GO:0046324)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|lung(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GAAGAGATCCCGCTGGGGGGA	0.672																																					p.R99L													.	FAM132A-68	0			c.G296T						.						27.0	35.0	32.0					1																	1179654		2185	4285	6470	SO:0001630	splice_region_variant	388581	exon3			AGATCCCGCTGGG	BC089443	CCDS30554.1	1p36.33	2012-03-26	2007-03-27	2007-03-27	ENSG00000184163	ENSG00000184163			32308	protein-coding gene	gene with protein product	"""adipolin"", ""adipose-derived insulin-sensitizing factor"""		"""C1q domain containing 2"""	C1QDC2		21849507	Standard	NM_001014980		Approved	MGC105127, C1QTNF12, CTRP12	uc001adl.2	Q5T7M4	OTTHUMG00000001412	ENST00000330388.2:c.295-1G>T	1.37:g.1179654C>A		Somatic	76	0		WXS	Illumina HiSeq		20	4	NM_001014980	0	0	0	0	0	Q5EBL5	Missense_Mutation	SNP	ENST00000330388.2	37	CCDS30554.1	.	.	.	.	.	.	.	.	.	.	c	15.92	2.973867	0.53720	.	.	ENSG00000184163	ENST00000330388	T	0.42900	0.96	3.76	1.7	0.24286	.	0.794942	0.10532	N	0.663663	T	0.42630	0.1211	M	0.69823	2.125	0.80722	D	1	P	0.46064	0.872	P	0.45377	0.478	T	0.32348	-0.9910	10	0.24483	T	0.36	.	5.7602	0.18196	0.0:0.7224:0.0:0.2776	.	99	Q5T7M4	F132A_HUMAN	L	99	ENSP00000329137:R99L	ENSP00000329137:R99L	R	-	2	0	FAM132A	1169517	0.002000	0.14202	0.440000	0.26846	0.002000	0.02628	0.109000	0.15417	0.333000	0.23563	-0.417000	0.06048	CGG	.		0.672	FAM132A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004080.4	XM_371208	Missense_Mutation
XKR8	55113	ucsc.edu	37	1	28290011	28290011	+	Silent	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr1:28290011C>T	ENST00000373884.5	+	2	905	c.297C>T	c.(295-297)tgC>tgT	p.C99C		NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	99					engulfment of apoptotic cell (GO:0043652)|phosphatidylserine exposure on apoptotic cell surface (GO:0070782)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(1)	4		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;4.72e-24)|Colorectal(126;1.52e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00572)|READ - Rectum adenocarcinoma(331;0.0526)		TGCCTAGGTGCGTGCAGGAGC	0.607																																					p.C99C													.	XKR8-90	0			c.C297T						.						44.0	43.0	43.0					1																	28290011		2203	4300	6503	SO:0001819	synonymous_variant	55113	exon2			TAGGTGCGTGCAG	AK091615	CCDS315.1	1p35.3	2008-02-05	2006-01-12		ENSG00000158156	ENSG00000158156			25508	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 8"""			12477932	Standard	NM_018053		Approved	FLJ10307	uc001bph.1	Q9H6D3	OTTHUMG00000003912	ENST00000373884.5:c.297C>T	1.37:g.28290011C>T		Somatic	86	0		WXS	Illumina HiSeq		38	4	NM_018053	0	0	0	0	0		Silent	SNP	ENST00000373884.5	37	CCDS315.1																																																																																			.		0.607	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011175.1	NM_018053	
ZSCAN20	7579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	33960785	33960785	+	Silent	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr1:33960785C>T	ENST00000361328.3	+	8	2994	c.2841C>T	c.(2839-2841)atC>atT	p.I947I		NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	947					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CCAAGCTCATCACACACCAGA	0.527																																					p.I947I		.											.	ZSCAN20-93	0			c.C2841T						.						82.0	96.0	91.0					1																	33960785		2167	4282	6449	SO:0001819	synonymous_variant	7579	exon8			GCTCATCACACAC	X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"""-"", ""Zinc fingers, C2H2-type"""	13093	protein-coding gene	gene with protein product		611315	"""zinc finger protein 31 (KOX 29)"", ""zinc finger protein 31"""	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.2841C>T	1.37:g.33960785C>T		Somatic	108	0		WXS	Illumina HiSeq	Phase_I	39	36	NM_145238	0	0	0	0	0	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Silent	SNP	ENST00000361328.3	37	CCDS41300.1																																																																																			.		0.527	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238	
EIF2D	1939	ucsc.edu	37	1	206785684	206785684	+	Silent	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr1:206785684C>T	ENST00000271764.2	-	1	220	c.12G>A	c.(10-12)aaG>aaA	p.K4K	EIF2D_ENST00000367114.3_Silent_p.K4K	NM_006893.2	NP_008824.2	P41214	EIF2D_HUMAN	eukaryotic translation initiation factor 2D	4					formation of translation preinitiation complex (GO:0001731)|intracellular protein transport (GO:0006886)|IRES-dependent translational initiation (GO:0002192)|ribosome disassembly (GO:0032790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor activity (GO:0004872)|translation initiation factor activity (GO:0003743)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						CCCGAAAGGCCTTGGCAAACA	0.627																																					p.K4K													.	EIF2D-92	0			c.G12A						.						118.0	103.0	108.0					1																	206785684		2203	4300	6503	SO:0001819	synonymous_variant	1939	exon1			AAAGGCCTTGGCA	BC001585	CCDS1465.1, CCDS55680.1	1q32.1	2014-05-06	2011-01-19	2011-01-19	ENSG00000143486	ENSG00000143486			6583	protein-coding gene	gene with protein product		613709				20566627	Standard	NM_001201478		Approved	LGTN	uc001heh.2	P41214	OTTHUMG00000184619	ENST00000271764.2:c.12G>A	1.37:g.206785684C>T		Somatic	127	0		WXS	Illumina HiSeq		41	4	NM_006893	0	0	15	15	0	Q5SY40|Q8IXV3|Q96DG3|Q96TG7|Q9NR27|Q9NSN0|Q9NV18|Q9NZ21	Silent	SNP	ENST00000271764.2	37	CCDS1465.1																																																																																			.		0.627	EIF2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088475.1	NM_006893	
FAM71A	149647	broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	212799448	212799448	+	Missense_Mutation	SNP	G	G	T	rs149566937		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr1:212799448G>T	ENST00000294829.3	+	1	1660	c.1229G>T	c.(1228-1230)aGg>aTg	p.R410M	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	410						nucleus (GO:0005634)		p.R410K(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		CAGCATGGAAGGGAGCGAACC	0.627																																					p.R410M													.	FAM71A-94	1	Substitution - Missense(1)	skin(1)	c.G1229T						.						53.0	59.0	57.0					1																	212799448		2203	4300	6503	SO:0001583	missense	149647	exon1			ATGGAAGGGAGCG		CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.1229G>T	1.37:g.212799448G>T	ENSP00000294829:p.Arg410Met	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	30	23	NM_153606	0	0	0	0	0	Q5VTZ1	Missense_Mutation	SNP	ENST00000294829.3	37	CCDS1507.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.283252	0.23392	.	.	ENSG00000162771	ENST00000294829;ENST00000545975	T	0.03889	3.77	4.31	-3.37	0.04898	.	.	.	.	.	T	0.02193	0.0068	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.12156	0.007	T	0.43814	-0.9368	9	0.54805	T	0.06	-8.0E-4	2.7678	0.05325	0.1371:0.2773:0.445:0.1406	.	410	Q8IYT1	FA71A_HUMAN	M	410;185	ENSP00000294829:R410M	ENSP00000294829:R410M	R	+	2	0	FAM71A	210866071	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.825000	0.04433	-0.780000	0.04553	-0.152000	0.13540	AGG	.		0.627	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606	
URB2	9816	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	229770859	229770859	+	Missense_Mutation	SNP	G	G	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr1:229770859G>C	ENST00000258243.2	+	4	635	c.499G>C	c.(499-501)Gcc>Ccc	p.A167P		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	167						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						AGCTGTGGTAGCCCAGTTGTT	0.582																																					p.A167P		.											.	URB2-174	0			c.G499C						.						68.0	55.0	59.0					1																	229770859		2203	4300	6503	SO:0001583	missense	9816	exon4			GTGGTAGCCCAGT	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.499G>C	1.37:g.229770859G>C	ENSP00000258243:p.Ala167Pro	Somatic	104	1		WXS	Illumina HiSeq	Phase_I	25	20	NM_014777	0	0	0	0	0	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	G	3.088	-0.187511	0.06299	.	.	ENSG00000135763	ENST00000258243	T	0.10005	2.92	5.68	1.37	0.22104	.	0.578081	0.19373	N	0.115852	T	0.03783	0.0107	N	0.04043	-0.29	0.18873	N	0.999984	B	0.15930	0.015	B	0.14023	0.01	T	0.43734	-0.9373	9	.	.	.	-6.523	4.8515	0.13538	0.0761:0.3087:0.4376:0.1776	.	167	Q14146	URB2_HUMAN	P	167	ENSP00000258243:A167P	.	A	+	1	0	URB2	227837482	0.067000	0.21026	0.009000	0.14445	0.226000	0.24999	0.674000	0.25218	0.406000	0.25560	0.650000	0.86243	GCC	.		0.582	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
URB2	9816	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	229770863	229770863	+	Missense_Mutation	SNP	A	A	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr1:229770863A>G	ENST00000258243.2	+	4	639	c.503A>G	c.(502-504)cAg>cGg	p.Q168R		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	168						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						GTGGTAGCCCAGTTGTTTGAG	0.582																																					p.Q168R		.											.	URB2-174	0			c.A503G						.						68.0	55.0	59.0					1																	229770863		2203	4300	6503	SO:0001583	missense	9816	exon4			TAGCCCAGTTGTT	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.503A>G	1.37:g.229770863A>G	ENSP00000258243:p.Gln168Arg	Somatic	105	0		WXS	Illumina HiSeq	Phase_I	26	21	NM_014777	0	0	0	0	0	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	A	9.721	1.159761	0.21454	.	.	ENSG00000135763	ENST00000258243	T	0.09817	2.94	5.68	0.193	0.15139	.	0.485156	0.24580	N	0.037302	T	0.09512	0.0234	L	0.56769	1.78	0.22226	N	0.999273	P	0.35077	0.483	B	0.30251	0.113	T	0.20571	-1.0271	9	.	.	.	-5.5473	9.3827	0.38325	0.4958:0.3913:0.0:0.1129	.	168	Q14146	URB2_HUMAN	R	168	ENSP00000258243:Q168R	.	Q	+	2	0	URB2	227837486	0.984000	0.35163	0.009000	0.14445	0.428000	0.31595	1.413000	0.34725	0.129000	0.18514	0.528000	0.53228	CAG	.		0.582	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
MCM10	55388	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	13222572	13222572	+	Missense_Mutation	SNP	A	A	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr10:13222572A>C	ENST00000484800.2	+	7	1001	c.898A>C	c.(898-900)Ata>Cta	p.I300L	MCM10_ENST00000378694.1_Missense_Mutation_p.I299L|MCM10_ENST00000378714.3_Missense_Mutation_p.I299L			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	300	OB-fold domain. {ECO:0000250}.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						ATTTGGGGTTATATTGAAGAA	0.423																																					p.I300L		.											.	MCM10-653	0			c.A898C						.						232.0	230.0	231.0					10																	13222572		2203	4300	6503	SO:0001583	missense	55388	exon7			GGGGTTATATTGA	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.898A>C	10.37:g.13222572A>C	ENSP00000418268:p.Ile300Leu	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	192	88	NM_182751	0	0	0	0	0	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	A	10.70	1.422993	0.25639	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.16073	2.38;2.37;2.37	5.82	5.82	0.92795	.	0.103877	0.64402	D	0.000003	T	0.16257	0.0391	N	0.26042	0.785	0.53688	D	0.999971	B;B;B	0.22683	0.037;0.073;0.008	B;B;B	0.30029	0.061;0.11;0.041	T	0.05683	-1.0870	10	0.36615	T	0.2	-11.6005	16.1814	0.81903	1.0:0.0:0.0:0.0	.	299;299;300	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	L	299;300;300;299	ENSP00000367986:I299L;ENSP00000418268:I300L;ENSP00000367966:I299L	ENSP00000354945:I300L	I	+	1	0	MCM10	13262578	1.000000	0.71417	0.940000	0.37924	0.594000	0.36715	4.284000	0.58983	2.234000	0.73211	0.533000	0.62120	ATA	.		0.423	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
PCBD1	5092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	72643783	72643783	+	Missense_Mutation	SNP	T	T	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr10:72643783T>C	ENST00000299299.3	-	4	489	c.239A>G	c.(238-240)cAt>cGt	p.H80R	PCBD1_ENST00000493228.1_5'UTR	NM_000281.2	NP_000272.1	P61457	PHS_HUMAN	pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha	80	Substrate binding. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein homotetramerization (GO:0051289)|regulation of protein homodimerization activity (GO:0043496)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	4-alpha-hydroxytetrahydrobiopterin dehydratase activity (GO:0008124)|identical protein binding (GO:0042802)|phenylalanine 4-monooxygenase activity (GO:0004505)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|large_intestine(1)	4						GGCACACTCATGGGTGCTCAG	0.512																																					p.H80R		.											.	PCBD1-90	0			c.A239G						.						94.0	76.0	82.0					10																	72643783		2203	4300	6503	SO:0001583	missense	5092	exon4			CACTCATGGGTGC	BC006324	CCDS31217.1	10q22	2014-04-01	2007-11-06	2005-02-11	ENSG00000166228	ENSG00000166228	4.2.1.96		8646	protein-coding gene	gene with protein product	"""Pterin-4a-carbinolamine dehydratase (dimerization cofactor of hepatic nuclear factor 1-alpha)"", ""pterin-4-alpha carbinolamine dehydratase"", ""dimerizing cofactor for HNF1"""	126090	"""6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1)"", ""pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1)"""	DCOH, PCBD		8486378	Standard	XM_005269877		Approved	PCD	uc001jrn.1	P61457	OTTHUMG00000018417	ENST00000299299.3:c.239A>G	10.37:g.72643783T>C	ENSP00000299299:p.His80Arg	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	61	20	NM_000281	0	0	87	211	124	P70519|P80095|Q9D930	Missense_Mutation	SNP	ENST00000299299.3	37	CCDS31217.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.375645	0.61735	.	.	ENSG00000166228	ENST00000299299	D	0.92752	-3.1	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97801	0.9278	H	0.98333	4.205	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99478	1.0947	10	0.87932	D	0	.	15.9584	0.79906	0.0:0.0:0.0:1.0	.	80	P61457	PHS_HUMAN	R	80	ENSP00000299299:H80R	ENSP00000299299:H80R	H	-	2	0	PCBD1	72313789	1.000000	0.71417	0.978000	0.43139	0.159000	0.22180	7.474000	0.81024	2.165000	0.68154	0.528000	0.53228	CAT	.		0.512	PCBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048527.1	NM_000281	
ADAM8	101	ucsc.edu	37	10	135080899	135080899	+	Missense_Mutation	SNP	G	G	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr10:135080899G>A	ENST00000445355.3	-	21	2326	c.2276C>T	c.(2275-2277)cCa>cTa	p.P759L	ADAM8_ENST00000415217.3_Silent_p.P703P|ADAM8_ENST00000485491.2_Missense_Mutation_p.P694L	NM_001109.4	NP_001100.3	P78325	ADAM8_HUMAN	ADAM metallopeptidase domain 8	759					activation of MAPK activity involved in innate immune response (GO:0035419)|angiogenesis (GO:0001525)|cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration involved in inflammatory response (GO:0002523)|lymphocyte chemotaxis (GO:0048247)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell adhesion (GO:0045785)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of fibronectin-dependent thymocyte migration (GO:2000415)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neutrophil extravasation (GO:2000391)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein processing (GO:0010954)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|regulation of cell-cell adhesion (GO:0022407)|single organismal cell-cell adhesion (GO:0016337)	alpha9-beta1 integrin-ADAM8 complex (GO:0071133)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dense core granule membrane (GO:0032127)|integral component of plasma membrane (GO:0005887)|phagolysosome (GO:0032010)|plasma membrane (GO:0005886)|podosome (GO:0002102)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein self-association (GO:0043621)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)	17		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		TGGGAAGGGTGGGCTGGACAC	0.662																																					p.P759L													.	ADAM8-90	0			c.C2276T						.						99.0	78.0	85.0					10																	135080899		2198	4298	6496	SO:0001583	missense	101	exon21			AAGGGTGGGCTGG	D26579	CCDS31319.2, CCDS58102.1, CCDS58103.1	10q26.3	2014-03-20	2005-08-18		ENSG00000151651	ENSG00000151651		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	215	protein-coding gene	gene with protein product		602267	"""a disintegrin and metalloproteinase domain 8"""			9126482	Standard	NM_001109		Approved	CD156, MS2, CD156a	uc021qbe.1	P78325	OTTHUMG00000019309	ENST00000445355.3:c.2276C>T	10.37:g.135080899G>A	ENSP00000453302:p.Pro759Leu	Somatic	48	0		WXS	Illumina HiSeq		37	4	NM_001109	0	0	3	3	0	B4DVM6|H0YL36|H0YLR0|H0YN39	Missense_Mutation	SNP	ENST00000445355.3	37	CCDS31319.2																																																																																			.		0.662	ADAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051118.4	NM_001109	
OR4C13	283092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	49974076	49974076	+	Silent	SNP	C	C	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr11:49974076C>A	ENST00000555099.1	+	1	134	c.102C>A	c.(100-102)atC>atA	p.I34I		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	34						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						TCATCTACATCAACGCCATGA	0.413																																					p.I34I		.											.	OR4C13-72	0			c.C102A						.						206.0	190.0	195.0					11																	49974076		2201	4296	6497	SO:0001819	synonymous_variant	283092	exon1			CTACATCAACGCC	AB065750	CCDS31495.1	11p11.12	2012-10-03			ENSG00000258817	ENSG00000258817		"""GPCR / Class A : Olfactory receptors"""	15169	protein-coding gene	gene with protein product							Standard	NM_001001955		Approved		uc010rhz.2	Q8NGP0	OTTHUMG00000166686	ENST00000555099.1:c.102C>A	11.37:g.49974076C>A		Somatic	299	0		WXS	Illumina HiSeq	Phase_I	307	35	NM_001001955	0	0	0	0	0	A6NJJ3|B9EH30|Q6IF48|Q96R68	Silent	SNP	ENST00000555099.1	37	CCDS31495.1																																																																																			.		0.413	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955	
NUMA1	4926	broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	71723991	71723991	+	Missense_Mutation	SNP	G	G	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr11:71723991G>T	ENST00000393695.3	-	15	4889	c.4558C>A	c.(4558-4560)Ctg>Atg	p.L1520M	NUMA1_ENST00000351960.6_Intron|NUMA1_ENST00000358965.6_Missense_Mutation_p.L1520M|RP11-849H4.4_ENST00000502284.1_RNA	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						CTCTCCTCCAGGACCTTGACC	0.602			T	RARA	APL																																p.L1520M				Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1-633	0			c.C4558A						.						108.0	100.0	102.0					11																	71723991		2200	4293	6493	SO:0001583	missense	4926	exon15			CCTCCAGGACCTT	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.4558C>A	11.37:g.71723991G>T	ENSP00000377298:p.Leu1520Met	Somatic	130	0		WXS	Illumina HiSeq	Phase_I	60	22	NM_006185	0	1	81	152	70		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.799598	0.50208	.	.	ENSG00000137497	ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	T;T	0.15139	2.45;2.48	5.0	3.1	0.35709	.	0.000000	0.41938	D	0.000795	T	0.23688	0.0573	L	0.27053	0.805	0.27491	N	0.952288	D;D;D;D	0.89917	1.0;0.997;0.999;1.0	D;D;D;D	0.78314	0.989;0.991;0.976;0.989	T	0.01545	-1.1328	10	0.72032	D	0.01	.	6.9885	0.24741	0.157:0.1418:0.7011:0.0	.	1526;1004;1520;1520	Q4LE64;Q59HB8;Q14980-2;Q14980	.;.;.;NUMA1_HUMAN	M	1520;1520;1083;489	ENSP00000351851:L1520M;ENSP00000377298:L1520M	ENSP00000351851:L1520M	L	-	1	2	NUMA1	71401639	0.819000	0.29175	1.000000	0.80357	0.991000	0.79684	1.055000	0.30467	1.336000	0.45506	0.561000	0.74099	CTG	.		0.602	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
HEBP1	50865	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	13140120	13140120	+	Missense_Mutation	SNP	T	T	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:13140120T>C	ENST00000014930.4	-	3	522	c.364A>G	c.(364-366)Att>Gtt	p.I122V	HEBP1_ENST00000536942.1_Missense_Mutation_p.I122V|RP11-392P7.6_ENST00000499948.2_RNA	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1	122					circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		CGTTCCTCAATCTTAACGCTT	0.483																																					p.I122V		.											.	HEBP1-135	0			c.A364G						.						179.0	158.0	165.0					12																	13140120		2203	4300	6503	SO:0001583	missense	50865	exon3			CCTCAATCTTAAC	AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"""Endogenous ligands"""	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771	ENST00000014930.4:c.364A>G	12.37:g.13140120T>C	ENSP00000014930:p.Ile122Val	Somatic	211	0		WXS	Illumina HiSeq	Phase_I	187	75	NM_015987	0	0	42	88	46	A8K1G2|Q9Y5Z5	Missense_Mutation	SNP	ENST00000014930.4	37	CCDS31749.1	.	.	.	.	.	.	.	.	.	.	T	11.41	1.631678	0.29068	.	.	ENSG00000013583	ENST00000014930;ENST00000535636;ENST00000536942	T;T;T	0.25579	1.79;1.79;1.79	5.66	4.45	0.53987	Regulatory factor, effector, bacterial (1);	0.047188	0.85682	D	0.000000	T	0.33527	0.0866	M	0.77313	2.365	0.47737	D	0.9995	B	0.22746	0.074	B	0.32762	0.152	T	0.12192	-1.0557	10	0.27082	T	0.32	-5.125	12.5735	0.56352	0.1242:0.0:0.0:0.8758	.	122	Q9NRV9	HEBP1_HUMAN	V	122;51;122	ENSP00000014930:I122V;ENSP00000442020:I51V;ENSP00000441678:I122V	ENSP00000014930:I122V	I	-	1	0	HEBP1	13031387	1.000000	0.71417	0.882000	0.34594	0.210000	0.24377	3.727000	0.54984	2.283000	0.76528	0.533000	0.62120	ATT	.		0.483	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1		
PPFIBP1	8496	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	27809595	27809595	+	Missense_Mutation	SNP	A	A	C	rs369414467		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:27809595A>C	ENST00000318304.8	+	10	1119	c.836A>C	c.(835-837)gAa>gCa	p.E279A	PPFIBP1_ENST00000542629.1_Missense_Mutation_p.E248A|PPFIBP1_ENST00000228425.6_Missense_Mutation_p.E248A|PPFIBP1_ENST00000537927.1_Missense_Mutation_p.E126A	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	279					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					AAGGAATCTGAAGTAAAAAGG	0.313																																					p.E279A		.											.	PPFIBP1-228	0			c.A836C						.						73.0	76.0	75.0					12																	27809595		2203	4299	6502	SO:0001583	missense	8496	exon10			AATCTGAAGTAAA	AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.836A>C	12.37:g.27809595A>C	ENSP00000314724:p.Glu279Ala	Somatic	113	0		WXS	Illumina HiSeq	Phase_I	176	79	NM_177444	0	0	31	51	20	O75336|Q86X70|Q9NY03|Q9ULJ0	Missense_Mutation	SNP	ENST00000318304.8	37	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	A	14.99	2.699998	0.48307	.	.	ENSG00000110841	ENST00000543820;ENST00000545381;ENST00000540114;ENST00000537927;ENST00000318304;ENST00000542629;ENST00000228425	T;T;T;T;T;T	0.59083	0.29;0.62;0.71;1.19;1.2;1.61	5.05	5.05	0.67936	.	0.000000	0.35151	U	0.003420	T	0.56645	0.1999	L	0.38953	1.18	0.41614	D	0.988929	P;B;P;B	0.44776	0.828;0.044;0.843;0.073	P;B;B;B	0.49477	0.612;0.027;0.384;0.06	T	0.57940	-0.7724	10	0.42905	T	0.14	-26.9289	13.3332	0.60500	1.0:0.0:0.0:0.0	.	126;279;248;248	Q86W92-3;Q86W92;Q86W92-2;Q86W92-4	.;LIPB1_HUMAN;.;.	A	250;248;107;126;279;248;248	ENSP00000445822:E248A;ENSP00000444304:E107A;ENSP00000445425:E126A;ENSP00000314724:E279A;ENSP00000443442:E248A;ENSP00000228425:E248A	ENSP00000228425:E248A	E	+	2	0	PPFIBP1	27700862	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	6.463000	0.73530	2.022000	0.59522	0.533000	0.62120	GAA	.		0.313	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	
GPD1	2819	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	50503242	50503242	+	Nonsense_Mutation	SNP	C	C	G	rs116736822	byFrequency	TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:50503242C>G	ENST00000301149.3	+	8	1222	c.990C>G	c.(988-990)taC>taG	p.Y330*	GPD1_ENST00000548814.1_Nonsense_Mutation_p.Y307*|COX14_ENST00000550487.1_5'Flank|COX14_ENST00000550654.1_5'Flank|COX14_ENST00000548985.1_5'Flank|RP4-605O3.4_ENST00000552815.1_RNA|COX14_ENST00000317943.2_5'Flank	NM_001257199.1|NM_005276.3	NP_001244128.1|NP_005267.2	P21695	GPDA_HUMAN	glycerol-3-phosphate dehydrogenase 1 (soluble)	330					cellular lipid metabolic process (GO:0044255)|cellular response to cAMP (GO:0071320)|cellular response to tumor necrosis factor (GO:0071356)|gluconeogenesis (GO:0006094)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophosphate shuttle (GO:0006127)|glycerophospholipid biosynthetic process (GO:0046474)|NADH oxidation (GO:0006116)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrion (GO:0005739)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|NAD binding (GO:0051287)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						AGGTGTGCTACGAGGGCCAGC	0.577																																					p.Y330X	NSCLC(141;1402 1905 9497 13391 44868)	.											.	GPD1-90	0			c.C990G						.						139.0	108.0	118.0					12																	50503242		2203	4300	6503	SO:0001587	stop_gained	2819	exon8			GTGCTACGAGGGC		CCDS8799.1, CCDS58229.1	12q13.12	2013-09-20			ENSG00000167588	ENSG00000167588	1.1.1.8		4455	protein-coding gene	gene with protein product		138420					Standard	NM_005276		Approved		uc001rvz.4	P21695	OTTHUMG00000169813	ENST00000301149.3:c.990C>G	12.37:g.50503242C>G	ENSP00000301149:p.Tyr330*	Somatic	135	0		WXS	Illumina HiSeq	Phase_I	87	26	NM_005276	0	0	0	1	1	F8W1L5|Q8N1B0	Nonsense_Mutation	SNP	ENST00000301149.3	37	CCDS8799.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.796601	0.90453	.	.	ENSG00000167588	ENST00000301149;ENST00000548814	.	.	.	4.99	-5.7	0.02421	.	0.125588	0.53938	D	0.000044	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.4578	14.9665	0.71198	0.0:0.6296:0.0:0.3704	.	.	.	.	X	330;307	.	ENSP00000301149:Y330X	Y	+	3	2	GPD1	48789509	0.008000	0.16893	0.884000	0.34674	0.899000	0.52679	-0.879000	0.04188	-1.358000	0.02177	-0.379000	0.06801	TAC	C|0.998;T|0.002		0.577	GPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406018.1		
LRIG3	121227	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	59271290	59271290	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:59271290C>A	ENST00000320743.3	-	15	2714	c.2428G>T	c.(2428-2430)Gtc>Ttc	p.V810F	LRIG3_ENST00000379141.4_Missense_Mutation_p.V750F	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	810					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			ATGATCACGACACCCACAGTG	0.562			T	ROS1	NSCLC																																p.V810F		.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3-229	0			c.G2428T						.						212.0	121.0	152.0					12																	59271290		2203	4300	6503	SO:0001583	missense	121227	exon15			TCACGACACCCAC	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"""Immunoglobulin superfamily / I-set domain containing"""	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.2428G>T	12.37:g.59271290C>A	ENSP00000326759:p.Val810Phe	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	61	39	NM_153377	0	0	4	11	7	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	37	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.675366	0.47781	.	.	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.61040	0.18;0.14	5.59	3.74	0.42951	.	0.494270	0.15041	N	0.283853	T	0.47414	0.1444	L	0.47716	1.5	0.39938	D	0.974378	P;P	0.39665	0.682;0.624	B;B	0.37508	0.252;0.154	T	0.36212	-0.9757	9	.	.	.	.	8.2502	0.31712	0.0:0.6658:0.0:0.3342	.	750;810	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	F	750;810	ENSP00000368436:V750F;ENSP00000326759:V810F	.	V	-	1	0	LRIG3	57557557	1.000000	0.71417	0.987000	0.45799	0.819000	0.46315	2.549000	0.45803	0.796000	0.33947	0.655000	0.94253	GTC	.		0.562	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377	
ANKRD13A	88455	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	110457067	110457067	+	Missense_Mutation	SNP	T	T	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:110457067T>C	ENST00000261739.4	+	6	834	c.668T>C	c.(667-669)gTt>gCt	p.V223A	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	223						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						AGCAGGGAAGTTGAGCGGCGG	0.438																																					p.V223A		.											.	ANKRD13A-90	0			c.T668C						.						76.0	76.0	76.0					12																	110457067		2203	4300	6503	SO:0001583	missense	88455	exon6			GGGAAGTTGAGCG	AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"""Ankyrin repeat domain containing"""	21268	protein-coding gene	gene with protein product		615123	"""ankyrin repeat domain 13"""	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.668T>C	12.37:g.110457067T>C	ENSP00000261739:p.Val223Ala	Somatic	114	0		WXS	Illumina HiSeq	Phase_I	92	39	NM_033121	0	0	18	38	20	O60736	Missense_Mutation	SNP	ENST00000261739.4	37	CCDS9140.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.543716	0.65198	.	.	ENSG00000076513	ENST00000261738;ENST00000261739	T	0.65364	-0.15	5.83	5.83	0.93111	.	0.052948	0.85682	D	0.000000	T	0.73567	0.3603	M	0.72894	2.215	0.80722	D	1	D;D;D	0.56746	0.977;0.977;0.977	P;P;P	0.55011	0.766;0.766;0.766	T	0.77107	-0.2710	10	0.72032	D	0.01	-13.8298	15.3732	0.74584	0.0:0.0:0.0:1.0	.	223;223;223	B4DYP5;Q3ZTS7;Q8IZ07	.;.;AN13A_HUMAN	A	8;223	ENSP00000261739:V223A	ENSP00000261738:V8A	V	+	2	0	ANKRD13A	108941450	1.000000	0.71417	0.945000	0.38365	0.982000	0.71751	6.241000	0.72369	2.229000	0.72834	0.482000	0.46254	GTT	.		0.438	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121	
N4BP2L2	10443	broad.mit.edu	37	13	33095588	33095588	+	Splice_Site	SNP	T	T	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr13:33095588T>C	ENST00000267068.3	-	5	1638		c.e5-2		N4BP2L2_ENST00000446957.2_Splice_Site|N4BP2L2_ENST00000357505.6_Splice_Site|N4BP2L2_ENST00000504114.1_Splice_Site|N4BP2L2_ENST00000399396.3_Splice_Site	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2						negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		TCCTATGGCCTACACAAAGGA	0.338																																					.													.	N4BP2L2-68	0			c.187-2A>G						.						63.0	63.0	63.0					13																	33095588		2203	4299	6502	SO:0001630	splice_region_variant	10443	exon6			ATGGCCTACACAA	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"""phosphonoformate immuno-associated protein 5"""	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.1474-2A>G	13.37:g.33095588T>C		Somatic	101	0		WXS	Illumina HiSeq	Phase_I	122	4	NM_033111	0	0	5	5	0	A3KME8	Splice_Site	SNP	ENST00000267068.3	37	CCDS9346.1	.	.	.	.	.	.	.	.	.	.	T	19.63	3.863912	0.71949	.	.	ENSG00000244754	ENST00000504114;ENST00000357505;ENST00000399396;ENST00000446957;ENST00000505213;ENST00000267068	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2988	0.82793	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	N4BP2L2	31993588	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.773000	0.62331	2.311000	0.77944	0.533000	0.62120	.	.		0.338	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887	Intron
FREM2	341640	broad.mit.edu	37	13	39422803	39422803	+	Silent	SNP	C	C	G	rs372745449		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr13:39422803C>G	ENST00000280481.7	+	8	6591	c.6375C>G	c.(6373-6375)tcC>tcG	p.S2125S	FREM2_ENST00000482551.1_3'UTR	NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2125	Calx-beta 4.				cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		ACTCTGTCTCCGATTGTGAGT	0.358																																					p.S2125S													.	FREM2-100	0			c.C6375G						.						53.0	51.0	52.0					13																	39422803		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon8			TGTCTCCGATTGT	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.6375C>G	13.37:g.39422803C>G		Somatic	65	0		WXS	Illumina HiSeq	Phase_I	73	3	NM_207361	0	0	0	0	0	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			.		0.358	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
SIX4	51804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	61190290	61190290	+	Missense_Mutation	SNP	A	A	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr14:61190290A>C	ENST00000216513.4	-	1	562	c.503T>G	c.(502-504)aTc>aGc	p.I168S		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	168					anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		GCTCTCGAGGATGCTGTAGAG	0.692																																					p.I168S		.											.	SIX4-154	0			c.T503G						.						13.0	14.0	14.0					14																	61190290		2190	4286	6476	SO:0001583	missense	51804	exon1			TCGAGGATGCTGT	AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"""Homeoboxes / SINE class"""	10890	protein-coding gene	gene with protein product		606342	"""sine oculis homeobox (Drosophila) homolog 4"", ""sine oculis homeobox homolog 4 (Drosophila)"""			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.503T>G	14.37:g.61190290A>C	ENSP00000216513:p.Ile168Ser	Somatic	26	0		WXS	Illumina HiSeq	Phase_I	20	9	NM_017420	0	0	1	3	2	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	37	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	A	19.26	3.793861	0.70452	.	.	ENSG00000100625	ENST00000216513;ENST00000556952	D	0.94046	-3.34	3.63	3.63	0.41609	.	0.265948	0.36591	N	0.002504	D	0.93086	0.7799	M	0.70842	2.15	0.58432	D	0.999997	P;D	0.53312	0.84;0.959	P;P	0.47346	0.537;0.544	D	0.93446	0.6798	10	0.87932	D	0	.	12.4167	0.55498	1.0:0.0:0.0:0.0	.	160;168	G3V2N2;Q9UIU6	.;SIX4_HUMAN	S	168;160	ENSP00000216513:I168S	ENSP00000216513:I168S	I	-	2	0	SIX4	60260043	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.828000	0.92047	1.508000	0.48769	0.528000	0.53228	ATC	.		0.692	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2		
C15orf53	400359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	38988925	38988925	+	Silent	SNP	G	G	C	rs146995135	byFrequency	TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr15:38988925G>C	ENST00000318792.1	+	1	127	c.117G>C	c.(115-117)gcG>gcC	p.A39A		NM_207444.2	NP_997327.1	Q8NAA6	CO053_HUMAN	chromosome 15 open reading frame 53	39			A -> V (in dbSNP:rs11857596).							endometrium(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	6		all_cancers(109;1.75e-13)|all_epithelial(112;1.02e-11)|Lung NSC(122;1.9e-09)|all_lung(180;4.04e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;8.39e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0321)		GTCTCCAGGCGTCTGTTTGGA	0.542																																					p.A39A		.											.	C15orf53-492	0			c.G117C						.						96.0	95.0	95.0					15																	38988925		2200	4297	6497	SO:0001819	synonymous_variant	400359	exon1			CCAGGCGTCTGTT		CCDS10048.1	15q14	2007-11-21			ENSG00000175779	ENSG00000175779			33796	protein-coding gene	gene with protein product							Standard	NM_207444		Approved	FLJ35695	uc001zkf.1	Q8NAA6	OTTHUMG00000129841	ENST00000318792.1:c.117G>C	15.37:g.38988925G>C		Somatic	145	1		WXS	Illumina HiSeq	Phase_I	86	32	NM_207444	0	0	0	0	0		Silent	SNP	ENST00000318792.1	37	CCDS10048.1																																																																																			G|0.998;T|0.002		0.542	C15orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252081.1	NM_207444	
DTWD1	56986	broad.mit.edu	37	15	49926740	49926740	+	Missense_Mutation	SNP	T	T	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr15:49926740T>G	ENST00000251250.6	+	5	623	c.416T>G	c.(415-417)cTc>cGc	p.L139R	DTWD1_ENST00000415425.1_Missense_Mutation_p.L52R|DTWD1_ENST00000403028.3_Missense_Mutation_p.L139R|DTWD1_ENST00000558653.1_Missense_Mutation_p.L139R|DTWD1_ENST00000559223.1_3'UTR	NM_020234.5	NP_064619.2	Q8N5C7	DTWD1_HUMAN	DTW domain containing 1	139										endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;0.0384)		all cancers(107;3.27e-08)|GBM - Glioblastoma multiforme(94;7.6e-05)		TAGGTTGCACTCATTTTTCCT	0.299																																					p.L139R													.	DTWD1-226	0			c.T416G						.						42.0	46.0	45.0					15																	49926740		2195	4292	6487	SO:0001583	missense	56986	exon4			TTGCACTCATTTT	BC032535	CCDS10132.1	15q21.2	2005-08-09			ENSG00000104047	ENSG00000104047			30926	protein-coding gene	gene with protein product							Standard	NM_020234		Approved	MDS009, MGC111207	uc001zxs.3	Q8N5C7	OTTHUMG00000131567	ENST00000251250.6:c.416T>G	15.37:g.49926740T>G	ENSP00000251250:p.Leu139Arg	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	175	6	NM_001144955	0	0	0	0	0	Q567Q3|Q8WVG9|Q9NRU6	Missense_Mutation	SNP	ENST00000251250.6	37	CCDS10132.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.952871	0.34471	.	.	ENSG00000104047	ENST00000403028;ENST00000251250;ENST00000415425	T;T	0.32988	1.43;1.43	4.95	3.83	0.44106	DTW (1);	0.183686	0.47852	D	0.000204	T	0.58566	0.2131	M	0.88775	2.98	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77004	0.967;0.989	T	0.63341	-0.6659	9	.	.	.	-17.3922	10.7355	0.46122	0.0:0.0756:0.0:0.9244	.	52;139	Q8N5C7-2;Q8N5C7	.;DTWD1_HUMAN	R	139;139;52	ENSP00000385399:L139R;ENSP00000251250:L139R	.	L	+	2	0	DTWD1	47714032	1.000000	0.71417	0.636000	0.29352	0.001000	0.01503	6.843000	0.75384	0.843000	0.35070	-0.256000	0.11100	CTC	.		0.299	DTWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254431.2	NM_020234	
C16orf59	80178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	2511752	2511752	+	Silent	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr16:2511752C>T	ENST00000361837.4	+	5	675	c.610C>T	c.(610-612)Ctg>Ttg	p.L204L	C16orf59_ENST00000569496.1_Silent_p.L204L|C16orf59_ENST00000563531.1_Silent_p.L204L|RP11-715J22.4_ENST00000566085.1_lincRNA|C16orf59_ENST00000483320.1_Silent_p.L37L	NM_025108.2	NP_079384.2	Q7L2K0	CP059_HUMAN	chromosome 16 open reading frame 59	204										lung(1)|skin(1)|urinary_tract(1)	3		Ovarian(90;0.17)				CGACAGGCACCTGCTGCGGCT	0.607																																					p.L204L		.											.	C16orf59-90	0			c.C610T						.						50.0	56.0	54.0					16																	2511752		2001	4172	6173	SO:0001819	synonymous_variant	80178	exon5			AGGCACCTGCTGC	AK023971	CCDS10468.2	16p13.3	2008-10-30			ENSG00000162062	ENSG00000162062			25849	protein-coding gene	gene with protein product						12477932	Standard	XM_006720955		Approved	FLJ13909	uc002cqh.3	Q7L2K0	OTTHUMG00000128859	ENST00000361837.4:c.610C>T	16.37:g.2511752C>T		Somatic	137	1		WXS	Illumina HiSeq	Phase_I	113	29	NM_025108	0	0	0	0	0	B4DXD7|Q96H61|Q9H872	Silent	SNP	ENST00000361837.4	37	CCDS10468.2																																																																																			.		0.607	C16orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250802.3	NM_025108	
CES3	23491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	67000741	67000741	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr16:67000741C>A	ENST00000303334.4	+	8	1106	c.1035C>A	c.(1033-1035)aaC>aaA	p.N345K	CES3_ENST00000394037.1_Missense_Mutation_p.N345K|CES3_ENST00000543856.1_5'Flank	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	345						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		GTGTCAACAACCATGAGTTCA	0.582																																					p.N345K		.											.	CES3-517	0			c.C1035A						.						134.0	131.0	132.0					16																	67000741		2200	4300	6500	SO:0001583	missense	23491	exon8			CAACAACCATGAG	AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"""Carboxylesterases"""	1865	protein-coding gene	gene with protein product	"""esterase 31"", ""brain carboxylesterase BR3"""	605279	"""carboxylesterase 3 (brain)"""			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.1035C>A	16.37:g.67000741C>A	ENSP00000304782:p.Asn345Lys	Somatic	248	0		WXS	Illumina HiSeq	Phase_I	223	85	NM_024922	0	0	0	1	1	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Missense_Mutation	SNP	ENST00000303334.4	37	CCDS10826.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.991536	0.35131	.	.	ENSG00000172828	ENST00000303334;ENST00000394037	T;T	0.65549	-0.16;-0.16	3.97	-2.89	0.05665	Carboxylesterase, type B (1);	0.000000	0.43579	D	0.000560	T	0.40862	0.1134	N	0.20610	0.595	0.80722	D	1	P	0.37207	0.587	B	0.41174	0.349	T	0.33650	-0.9860	10	0.08179	T	0.78	.	11.2659	0.49110	0.0:0.6915:0.0:0.3085	.	345	Q6UWW8	EST3_HUMAN	K	345	ENSP00000304782:N345K;ENSP00000377602:N345K	ENSP00000304782:N345K	N	+	3	2	CES3	65558242	0.304000	0.24472	0.647000	0.29507	0.123000	0.20343	-0.234000	0.09028	-0.385000	0.07833	-0.809000	0.03173	AAC	.		0.582	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922	
FAM65A	79567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	67576026	67576026	+	Missense_Mutation	SNP	G	G	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr16:67576026G>A	ENST00000379312.3	+	13	1470	c.1349G>A	c.(1348-1350)cGg>cAg	p.R450Q	CTD-2012K14.2_ENST00000567122.1_RNA|FAM65A_ENST00000428437.2_Missense_Mutation_p.R460Q|FAM65A_ENST00000540839.3_Missense_Mutation_p.R466Q|CTD-2012K14.4_ENST00000564717.1_RNA|CTD-2012K14.3_ENST00000563083.1_RNA|FAM65A_ENST00000422602.2_Missense_Mutation_p.R466Q|FAM65A_ENST00000042381.4_Missense_Mutation_p.R446Q	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	450						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		CCCTACAGTCGGACTCTGAGC	0.632																																					p.R466Q		.											.	FAM65A-92	0			c.G1397A						.						75.0	71.0	72.0					16																	67576026		2198	4300	6498	SO:0001583	missense	79567	exon13			ACAGTCGGACTCT	AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.1349G>A	16.37:g.67576026G>A	ENSP00000368614:p.Arg450Gln	Somatic	139	0		WXS	Illumina HiSeq	Phase_I	155	35	NM_001193523	0	0	73	102	29	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	37	CCDS54028.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.517558	0.85495	.	.	ENSG00000039523	ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	T;T;T	0.32753	1.44;1.44;1.44	4.62	4.62	0.57501	.	0.467258	0.23181	N	0.051009	T	0.50137	0.1598	L	0.57536	1.79	0.54753	D	0.999984	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.39187	-0.9626	10	0.14252	T	0.57	-16.318	17.523	0.87792	0.0:0.0:1.0:0.0	.	460;466;450;466	B4DIM2;E9PBS3;Q6ZS17;B4DEQ9	.;.;FA65A_HUMAN;.	Q	450;446;466;460	ENSP00000368614:R450Q;ENSP00000042381:R446Q;ENSP00000400099:R466Q	ENSP00000042381:R446Q	R	+	2	0	FAM65A	66133527	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	7.569000	0.82380	2.149000	0.67028	0.442000	0.29010	CGG	.		0.632	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519	
CHMP1A	5119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	89717999	89717999	+	Missense_Mutation	SNP	G	G	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr16:89717999G>C	ENST00000397901.3	-	3	339	c.83C>G	c.(82-84)gCg>gGg	p.A28G	CHMP1A_ENST00000550102.1_Missense_Mutation_p.A28G|CHMP1A_ENST00000253475.5_Silent_p.G21G|CHMP1A_ENST00000547614.1_5'UTR|CHMP1A_ENST00000535997.2_5'UTR	NM_002768.3	NP_002759.2	Q9HD42	CHM1A_HUMAN	charged multivesicular body protein 1A	28					cytokinesis (GO:0000910)|gene silencing (GO:0016458)|mitotic chromosome condensation (GO:0007076)|negative regulation of transcription by glucose (GO:0045014)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|proteolysis (GO:0006508)|transcription, DNA-templated (GO:0006351)|vesicle-mediated transport (GO:0016192)	condensed nuclear chromosome (GO:0000794)|early endosome (GO:0005769)|endomembrane system (GO:0012505)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|nuclear matrix (GO:0016363)	metallopeptidase activity (GO:0008237)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|ovary(1)	3		all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.048)		GGCCTGCTCCGCCTTGGAGTC	0.572																																					p.A28G		.											.	.	0			c.C83G						.						76.0	85.0	82.0					16																	89717999		2034	4180	6214	SO:0001583	missense	5119	exon3			TGCTCCGCCTTGG	U58048	CCDS45552.1	16q24.3	2011-09-21	2011-09-21	2007-03-20	ENSG00000131165	ENSG00000131165		"""Charged multivesicular body proteins"""	8740	protein-coding gene	gene with protein product		164010	"""procollagen (type III) N-endopeptidase"", ""chromatin modifying protein 1A"""	PRSM1, PCOLN3		11559748, 11559747	Standard	NM_002768		Approved	KIAA0047, CHMP1, Vps46A	uc002fnu.4	Q9HD42	OTTHUMG00000169521	ENST00000397901.3:c.83C>G	16.37:g.89717999G>C	ENSP00000380998:p.Ala28Gly	Somatic	89	0		WXS	Illumina HiSeq	Phase_I	75	43	NM_002768	0	0	47	144	97	A2RU09|Q14468|Q15779|Q96G31	Missense_Mutation	SNP	ENST00000397901.3	37	CCDS45552.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.467907	0.43839	.	.	ENSG00000131165	ENST00000397901;ENST00000550102	T;T	0.72505	-0.66;-0.66	4.81	2.69	0.31865	.	.	.	.	.	T	0.55768	0.1941	.	.	.	0.80722	D	1	B	0.15141	0.012	B	0.23419	0.046	T	0.46233	-0.9206	7	.	.	.	-3.1301	9.7579	0.40515	0.0779:0.141:0.7812:0.0	.	28	Q9HD42	CHM1A_HUMAN	G	28	ENSP00000380998:A28G;ENSP00000449243:A28G	.	A	-	2	0	CHMP1A	88245500	1.000000	0.71417	0.633000	0.29310	0.764000	0.43329	5.816000	0.69222	1.132000	0.42129	0.655000	0.94253	GCG	.		0.572	CHMP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404581.1	NM_002768	
TVP23C	201158	ucsc.edu	37	17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr17:15457087C>T	ENST00000225576.3	-	3	247	c.152G>A	c.(151-153)tGt>tAt	p.C51Y	TVP23C_ENST00000428082.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000584811.1_5'UTR|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.C51Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.C51Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.C51Y|TVP23C_ENST00000519970.1_Intron	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)	51						integral component of membrane (GO:0016021)											ACAGAGAAGACAGACGATGAT	0.373																																					p.C51Y													.	.	0			c.G152A						.						274.0	265.0	268.0					17																	15457087		2203	4300	6503	SO:0001583	missense	201158	exon3			AGAAGACAGACGA	BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"""family with sequence similarity 18, member B2"""	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.152G>A	17.37:g.15457087C>T	ENSP00000225576:p.Cys51Tyr	Somatic	406	57		WXS	Illumina HiSeq		444	69	NM_145301	0	0	6	29	23	Q3LIC7	Missense_Mutation	SNP	ENST00000225576.3	37	CCDS11170.1	.	.	.	.	.	.	.	.	.	.	.	2.368	-0.344949	0.05208	.	.	ENSG00000259024;ENSG00000175106;ENSG00000175106;ENSG00000175106	ENST00000522212;ENST00000225576;ENST00000428082;ENST00000438826	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	4.47	4.47	0.54385	.	0.000000	0.85682	N	0.000000	T	0.02571	0.0078	N	0.00004	-3.335	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.0;0.002	T	0.38457	-0.9660	10	0.02654	T	1	-3.8701	9.492	0.38965	0.0:0.0877:0.0:0.9123	.	51;51;51	Q96ET8-2;Q96ET8-3;Q96ET8	.;.;F18B2_HUMAN	Y	51	ENSP00000429865:C51Y;ENSP00000225576:C51Y;ENSP00000406387:C51Y;ENSP00000413355:C51Y	ENSP00000225576:C51Y	C	-	2	0	RP11-726O12.1;FAM18B2	15397812	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	6.178000	0.71968	0.670000	0.31165	-0.442000	0.05670	TGT	.		0.373	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2	NM_145301	
SLC47A2	146802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	19610045	19610045	+	Missense_Mutation	SNP	C	C	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr17:19610045C>G	ENST00000325411.5	-	9	915	c.865G>C	c.(865-867)Ggc>Cgc	p.G289R	SLC47A2_ENST00000463318.1_5'UTR|SLC47A2_ENST00000350657.5_Missense_Mutation_p.G253R	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	289					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	AAGAAGGGGCCCCAGTCCTGC	0.607																																					p.G289R		.											.	SLC47A2-90	0			c.G865C						.						82.0	76.0	78.0					17																	19610045		2203	4300	6503	SO:0001583	missense	146802	exon9			AGGGGCCCCAGTC	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"""Solute carriers"""	26439	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 2"""	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.865G>C	17.37:g.19610045C>G	ENSP00000326671:p.Gly289Arg	Somatic	123	1		WXS	Illumina HiSeq	Phase_I	65	32	NM_152908	0	0	2	3	1	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Missense_Mutation	SNP	ENST00000325411.5	37	CCDS11211.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.083522	0.76642	.	.	ENSG00000180638	ENST00000350657;ENST00000325411;ENST00000456947;ENST00000433844	T;T;T	0.44881	1.42;1.44;0.91	5.36	1.97	0.26223	.	0.287013	0.38548	N	0.001645	T	0.40423	0.1116	N	0.21545	0.675	0.42575	D	0.993199	D;D;P	0.54397	0.966;0.966;0.643	P;P;B	0.56751	0.805;0.805;0.271	T	0.29397	-1.0013	10	0.56958	D	0.05	-13.785	9.866	0.41142	0.273:0.5943:0.1327:0.0	.	253;253;289	Q86VL8-3;Q86VL8-4;Q86VL8	.;.;S47A2_HUMAN	R	253;289;204;253	ENSP00000338084:G253R;ENSP00000326671:G289R;ENSP00000391848:G253R	ENSP00000326671:G289R	G	-	1	0	SLC47A2	19550637	1.000000	0.71417	0.979000	0.43373	0.936000	0.57629	4.157000	0.58144	0.709000	0.31976	0.462000	0.41574	GGC	.		0.607	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908	
ZNF207	7756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	30696350	30696350	+	Missense_Mutation	SNP	A	A	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr17:30696350A>T	ENST00000321233.6	+	10	1307	c.1153A>T	c.(1153-1155)Aat>Tat	p.N385Y	ZNF207_ENST00000394670.4_Missense_Mutation_p.N401Y|ZNF207_ENST00000341711.6_Missense_Mutation_p.N302Y|ZNF207_ENST00000394673.2_Missense_Mutation_p.N370Y|ZNF207_ENST00000342555.6_Missense_Mutation_p.N404Y|ZNF207_ENST00000577908.1_Missense_Mutation_p.N401Y	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	385	GLEBS.				attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			GTATCAACGTAATCTTCCTCG	0.502																																					p.N401Y		.											.	ZNF207-90	0			c.A1201T						.						102.0	101.0	101.0					17																	30696350		2203	4300	6503	SO:0001583	missense	7756	exon11			CAACGTAATCTTC	AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"""Zinc fingers, C2H2-type"""	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.1153A>T	17.37:g.30696350A>T	ENSP00000322777:p.Asn385Tyr	Somatic	117	0		WXS	Illumina HiSeq	Phase_I	96	48	NM_001098507	0	0	44	86	42	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Missense_Mutation	SNP	ENST00000321233.6	37	CCDS11271.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.710294	0.48517	.	.	ENSG00000010244	ENST00000394670;ENST00000394673;ENST00000394679;ENST00000321233;ENST00000341711;ENST00000342555	T;T	0.47177	0.87;0.85	5.55	5.55	0.83447	.	0.143629	0.64402	D	0.000010	T	0.60209	0.2251	L	0.40543	1.245	0.48762	D	0.999708	D;D;D;P;D	0.76494	0.972;0.972;0.972;0.924;0.999	P;P;P;P;D	0.83275	0.6;0.6;0.6;0.461;0.996	T	0.58137	-0.7689	10	0.37606	T	0.19	.	15.7019	0.77549	1.0:0.0:0.0:0.0	.	354;404;401;370;385	A8MTG3;Q59G94;E1P660;O43670-2;O43670	.;.;.;.;ZN207_HUMAN	Y	401;354;404;370;302;385	ENSP00000378165:N401Y;ENSP00000344913:N302Y	ENSP00000322777:N370Y	N	+	1	0	ZNF207	27720463	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.566000	0.67372	2.108000	0.64289	0.477000	0.44152	AAT	.		0.502	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2		
MPO	4353	ucsc.edu	37	17	56355333	56355333	+	Silent	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr17:56355333C>T	ENST00000225275.3	-	7	1235	c.1059G>A	c.(1057-1059)ctG>ctA	p.L353L	MPO_ENST00000578493.1_5'UTR|MPO_ENST00000340482.3_Silent_p.L385L	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	353					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	ACATGTTGCGCAGGTTCCTGG	0.637																																					p.L353L													.	MPO-156	0			c.G1059A						.						75.0	67.0	70.0					17																	56355333		2203	4300	6503	SO:0001819	synonymous_variant	4353	exon7			GTTGCGCAGGTTC		CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.1059G>A	17.37:g.56355333C>T		Somatic	93	0		WXS	Illumina HiSeq		43	4	NM_000250	0	0	0	0	0	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Silent	SNP	ENST00000225275.3	37	CCDS11604.1																																																																																			.		0.637	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1		
PPM1D	8493	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	58740837	58740837	+	Missense_Mutation	SNP	G	G	A	rs200809297		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr17:58740837G>A	ENST00000305921.3	+	6	1974	c.1742G>A	c.(1741-1743)cGa>cAa	p.R581Q	RNU6-623P_ENST00000363143.1_RNA	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1D	581					G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of cell proliferation (GO:0008285)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			CTCACCATGCGACGCAGACTT	0.443											OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.R581Q		.											.	PPM1D-227	0			c.G1742A						.						85.0	82.0	83.0					17																	58740837		2203	4300	6503	SO:0001583	missense	8493	exon6			CCATGCGACGCAG	U78305	CCDS11625.1	17q23.3	2014-09-17	2010-03-05		ENSG00000170836	ENSG00000170836		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9277	protein-coding gene	gene with protein product	"""wild-type p53-induced phosphatase 1"", ""protein phosphatase 2C, delta isoform"""	605100	"""protein phosphatase 1D magnesium-dependent, delta isoform"""			9177166	Standard	NM_003620		Approved	Wip1, PP2C-DELTA	uc002iyt.2	O15297		ENST00000305921.3:c.1742G>A	17.37:g.58740837G>A	ENSP00000306682:p.Arg581Gln	Somatic	109	0	1033	WXS	Illumina HiSeq	Phase_I	104	52	NM_003620	0	0	9	15	6	Q53XP4|Q6P991|Q8IVR6	Missense_Mutation	SNP	ENST00000305921.3	37	CCDS11625.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.564808	0.86439	.	.	ENSG00000170836	ENST00000305921	T	0.61158	0.13	5.98	5.01	0.66863	.	0.278410	0.34268	N	0.004118	T	0.66157	0.2761	L	0.34521	1.04	0.40466	D	0.980292	D	0.89917	1.0	D	0.63957	0.92	T	0.71721	-0.4507	10	0.87932	D	0	-2.6262	17.3117	0.87212	0.0:0.1253:0.8747:0.0	.	581	O15297	PPM1D_HUMAN	Q	581	ENSP00000306682:R581Q	ENSP00000306682:R581Q	R	+	2	0	PPM1D	56095619	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.144000	0.77357	1.522000	0.49001	0.591000	0.81541	CGA	G|0.999;A|0.001		0.443	PPM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449474.1	NM_003620	
SMAD7	4092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	46447887	46447887	+	Missense_Mutation	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr18:46447887C>T	ENST00000262158.2	-	4	1422	c.1136G>A	c.(1135-1137)cGg>cAg	p.R379Q	SMAD7_ENST00000589634.1_Missense_Mutation_p.R378Q|SMAD7_ENST00000591805.1_Missense_Mutation_p.R164Q|SMAD7_ENST00000585986.1_5'UTR	NM_001190821.1|NM_005904.3	NP_001177750.1|NP_005895.1	O15105	SMAD7_HUMAN	SMAD family member 7	379	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				adherens junction assembly (GO:0034333)|artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|cellular protein complex localization (GO:0034629)|cellular response to transforming growth factor beta stimulus (GO:0071560)|gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein stabilization (GO:0050821)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of cardiac muscle contraction (GO:0055117)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|response to laminar fluid shear stress (GO:0034616)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activin binding (GO:0048185)|beta-catenin binding (GO:0008013)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity (GO:0030617)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	10	Colorectal(1;0.0518)					GTCATTGGGCCGCTGCAGGCT	0.582																																					p.R379Q		.											.	SMAD7-414	0			c.G1136A						.						90.0	77.0	81.0					18																	46447887		2203	4300	6503	SO:0001583	missense	4092	exon4			TTGGGCCGCTGCA	AF010193	CCDS11936.1, CCDS54186.1, CCDS59317.1	18q21.1	2006-11-06	2006-11-06	2004-05-26	ENSG00000101665	ENSG00000101665		"""SMADs"""	6773	protein-coding gene	gene with protein product		602932	"""MAD, mothers against decapentaplegic homolog 7 (Drosophila)"", ""SMAD, mothers against DPP homolog 7 (Drosophila)"""	MADH8, MADH7		9256479, 9730599	Standard	NM_005904		Approved		uc002ldg.3	O15105	OTTHUMG00000132655	ENST00000262158.2:c.1136G>A	18.37:g.46447887C>T	ENSP00000262158:p.Arg379Gln	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	66	25	NM_005904	0	0	24	38	14	B7Z773|K7EQ10|O14740|Q6DK23	Missense_Mutation	SNP	ENST00000262158.2	37	CCDS11936.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380052	0.82682	.	.	ENSG00000101665	ENST00000545051;ENST00000262158	D	0.98792	-5.14	5.66	5.66	0.87406	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.97648	0.9229	N	0.05330	-0.07	0.80722	D	1	P;D	0.71674	0.68;0.998	B;D	0.79108	0.19;0.992	D	0.97332	0.9951	10	0.23891	T	0.37	.	19.7417	0.96234	0.0:1.0:0.0:0.0	.	379;191	O15105;B3KYA8	SMAD7_HUMAN;.	Q	164;379	ENSP00000262158:R379Q	ENSP00000262158:R379Q	R	-	2	0	SMAD7	44701885	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.972000	0.63756	2.658000	0.90341	0.591000	0.81541	CGG	.		0.582	SMAD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255906.1	NM_005904	
GATAD2A	54815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	19613195	19613195	+	Missense_Mutation	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr19:19613195C>T	ENST00000360315.3	+	11	1943	c.1631C>T	c.(1630-1632)aCg>aTg	p.T544M	GATAD2A_ENST00000358713.3_Missense_Mutation_p.T544M|GATAD2A_ENST00000429563.2_Missense_Mutation_p.T347M|GATAD2A_ENST00000404158.1_Missense_Mutation_p.T545M|GATAD2A_ENST00000537887.1_Missense_Mutation_p.T173M|GATAD2A_ENST00000252577.5_Missense_Mutation_p.T519M	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	544					anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						GTCCTGCACACGTTCAGTCCG	0.647																																					p.T544M		.											.	GATAD2A-90	0			c.C1631T						.						76.0	79.0	78.0					19																	19613195		2203	4300	6503	SO:0001583	missense	54815	exon11			TGCACACGTTCAG	AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"""GATA zinc finger domain containing"""	29989	protein-coding gene	gene with protein product	"""p66 alpha"""	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.1631C>T	19.37:g.19613195C>T	ENSP00000353463:p.Thr544Met	Somatic	182	0		WXS	Illumina HiSeq	Phase_I	93	36	NM_017660	0	0	23	46	23	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Missense_Mutation	SNP	ENST00000360315.3	37	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	C	16.57	3.160141	0.57368	.	.	ENSG00000167491	ENST00000360315;ENST00000252577;ENST00000537887;ENST00000404158;ENST00000358713;ENST00000429563	T;T;T;T	0.45668	1.43;1.48;1.43;0.89	5.23	5.23	0.72850	.	0.357947	0.31872	N	0.006930	T	0.56202	0.1969	L	0.47716	1.5	0.38138	D	0.938352	D;D;D	0.89917	0.994;0.998;1.0	P;P;P	0.61592	0.628;0.794;0.891	T	0.62248	-0.6894	10	0.72032	D	0.01	-26.0515	17.4151	0.87497	0.0:1.0:0.0:0.0	.	347;564;544	B4DKZ7;B5MC40;Q86YP4	.;.;P66A_HUMAN	M	544;519;173;564;544;347	ENSP00000353463:T544M;ENSP00000252577:T519M;ENSP00000351552:T544M;ENSP00000388416:T347M	ENSP00000252577:T519M	T	+	2	0	GATAD2A	19474195	1.000000	0.71417	0.929000	0.37066	0.486000	0.33341	4.956000	0.63645	2.452000	0.82932	0.585000	0.79938	ACG	.		0.647	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660	
ZNF30	90075	broad.mit.edu	37	19	35435141	35435141	+	Missense_Mutation	SNP	G	G	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr19:35435141G>C	ENST00000601142.1	+	5	1508	c.1271G>C	c.(1270-1272)gGg>gCg	p.G424A	ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000426813.2_Missense_Mutation_p.G343A|ZNF30_ENST00000439785.1_Missense_Mutation_p.G425A|ZNF30_ENST00000303586.7_Missense_Mutation_p.G425A			P17039	ZNF30_HUMAN	zinc finger protein 30	424					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		ATCCATACTGGGGAGAAACCC	0.468																																					p.G425A													.	ZNF30-24	0			c.G1274C						.						57.0	62.0	60.0					19																	35435141		2202	4300	6502	SO:0001583	missense	90075	exon5			ATACTGGGGAGAA	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.1271G>C	19.37:g.35435141G>C	ENSP00000469954:p.Gly424Ala	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	35	3	NM_001099438	0	0	5	5	0	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	.	.	.	.	.	.	.	.	.	.	g	15.92	2.976488	0.53720	.	.	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813;ENST00000342559	T;T	0.26373	1.74;1.74	2.29	1.22	0.21188	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32496	0.0831	L	0.46947	1.48	0.26401	N	0.976428	D;D	0.54772	0.961;0.968	P;P	0.55667	0.673;0.781	T	0.12578	-1.0542	9	0.87932	D	0	.	6.6602	0.23011	0.1595:0.0:0.8405:0.0	.	425;424	P17039-2;P17039	.;ZNF30_HUMAN	A	425;424;343;133	ENSP00000403441:G425A;ENSP00000416457:G343A	ENSP00000303889:G424A	G	+	2	0	ZNF30	40126981	0.138000	0.22547	0.390000	0.26220	0.106000	0.19336	0.531000	0.23052	0.297000	0.22615	0.404000	0.27445	GGG	.		0.468	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
PRR12	57479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	50097991	50097991	+	Silent	SNP	G	G	C	rs527711314		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr19:50097991G>C	ENST00000418929.2	+	4	411	c.399G>C	c.(397-399)tcG>tcC	p.S133S		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0	Pro-rich.						DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		TCTTCATCTCGGGTGCCCTGC	0.662																																					p.S133S		.											.	PRR12-70	0			c.G399C						.						27.0	32.0	31.0					19																	50097991		2036	4191	6227	SO:0001819	synonymous_variant	57479	exon4			CATCTCGGGTGCC	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.399G>C	19.37:g.50097991G>C		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	30	15	NM_020719	0	0	25	43	18	E9PB06|Q8N4J6	Silent	SNP	ENST00000418929.2	37	CCDS46143.1																																																																																			.		0.662	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719	
GEN1	348654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	17955658	17955658	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:17955658C>T	ENST00000381254.2	+	11	1406	c.1192C>T	c.(1192-1194)Cag>Tag	p.Q398*	SMC6_ENST00000402989.1_Intron|GEN1_ENST00000317402.7_Nonsense_Mutation_p.Q398*	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	398					DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TAATCAACTACAGCCAATTCG	0.348								Homologous recombination																													p.Q398X		.											.	GEN1-359	0			c.C1192T						.						98.0	106.0	103.0					2																	17955658		2203	4300	6503	SO:0001587	stop_gained	348654	exon11			CAACTACAGCCAA	AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"""Holliday junction resolvase"""	612449	"""Gen endonuclease homolog 1 (Drosophila)"""			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.1192C>T	2.37:g.17955658C>T	ENSP00000370653:p.Gln398*	Somatic	171	1		WXS	Illumina HiSeq	Phase_I	221	106	NM_182625	0	0	0	0	0	Q17RS9|Q6ZN37	Nonsense_Mutation	SNP	ENST00000381254.2	37	CCDS1691.1	.	.	.	.	.	.	.	.	.	.	C	36	5.818087	0.96982	.	.	ENSG00000178295	ENST00000317402;ENST00000381254;ENST00000528873;ENST00000536097	.	.	.	5.31	5.31	0.75309	.	0.081308	0.49916	D	0.000127	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-4.4681	18.5911	0.91212	0.0:1.0:0.0:0.0	.	.	.	.	X	398;398;169;35	.	ENSP00000318977:Q398X	Q	+	1	0	GEN1	17819139	1.000000	0.71417	0.999000	0.59377	0.588000	0.36517	3.562000	0.53777	2.478000	0.83669	0.650000	0.86243	CAG	.		0.348	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625	
GPR113	165082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	26532908	26532908	+	Silent	SNP	C	C	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:26532908C>A	ENST00000311519.1	-	13	3143	c.3144G>T	c.(3142-3144)gtG>gtT	p.V1048V	GPR113_ENST00000333478.6_Intron|GPR113_ENST00000541401.1_Intron|GPR113_ENST00000459892.1_Intron|GPR113_ENST00000421160.2_Intron	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	1048					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCAGCAACTCACCAGGGAGA	0.572																																					p.V1048V		.											.	GPR113-94	0			c.G3144T						.						78.0	77.0	77.0					2																	26532908		2203	4300	6503	SO:0001819	synonymous_variant	165082	exon13			GCAACTCACCAGG	AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"""-"", ""GPCR / Class B : Orphans"""	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.3144G>T	2.37:g.26532908C>A		Somatic	139	1		WXS	Illumina HiSeq	Phase_I	124	56	NM_001145168	0	0	0	0	0	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Silent	SNP	ENST00000311519.1	37	CCDS46239.1																																																																																			.		0.572	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835	
GFPT1	2673	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	69553334	69553334	+	Missense_Mutation	SNP	A	A	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:69553334A>T	ENST00000357308.4	-	20	2265	c.2087T>A	c.(2086-2088)gTg>gAg	p.V696E	GFPT1_ENST00000361060.5_Missense_Mutation_p.V678E	NM_001244710.1	NP_001231639.1	Q06210	GFPT1_HUMAN	glutamine--fructose-6-phosphate transaminase 1	696					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|circadian regulation of gene expression (GO:0032922)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glucosamine biosynthetic process (GO:0006042)|glutamine metabolic process (GO:0006541)|negative regulation of glycogen biosynthetic process (GO:0045719)|post-translational protein modification (GO:0043687)|protein homotetramerization (GO:0051289)|protein N-linked glycosylation via asparagine (GO:0018279)|response to sucrose (GO:0009744)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			endometrium(1)|large_intestine(3)|lung(5)|skin(3)	12						CTCTACAGTCACAGATTTGGC	0.343																																					p.V696E		.											.	GFPT1-91	0			c.T2087A						.						89.0	90.0	90.0					2																	69553334		2203	4300	6503	SO:0001583	missense	2673	exon20			ACAGTCACAGATT		CCDS33216.1, CCDS58713.1	2p13	2014-09-17	2010-05-11		ENSG00000198380	ENSG00000198380	2.6.1.16		4241	protein-coding gene	gene with protein product		138292	"""glutamine-fructose-6-phosphate transaminase 1"""	GFPT		1460020	Standard	NM_002056		Approved	GFAT, GFA, GFAT1	uc002sfi.2	Q06210	OTTHUMG00000152666	ENST00000357308.4:c.2087T>A	2.37:g.69553334A>T	ENSP00000349860:p.Val696Glu	Somatic	46	0		WXS	Illumina HiSeq	Phase_I	60	22	NM_001244710	0	0	25	35	10	Q53QE6|Q9BXF8	Missense_Mutation	SNP	ENST00000357308.4	37	CCDS58713.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.559990	0.86335	.	.	ENSG00000198380	ENST00000357308;ENST00000361060	T;T	0.77358	-1.09;-1.09	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.93684	0.7982	H	0.99732	4.735	0.80722	D	1	D	0.65815	0.995	D	0.85130	0.997	D	0.96269	0.9197	10	0.87932	D	0	-14.7507	14.9534	0.71091	1.0:0.0:0.0:0.0	.	678	Q06210-2	.	E	696;678	ENSP00000349860:V696E;ENSP00000354347:V678E	ENSP00000349860:V696E	V	-	2	0	GFPT1	69406838	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	9.082000	0.94059	2.302000	0.77476	0.533000	0.62120	GTG	.		0.343	GFPT1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
NCKAP5	344148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	133541732	133541732	+	Missense_Mutation	SNP	C	C	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:133541732C>G	ENST00000409261.1	-	14	3025	c.2652G>C	c.(2650-2652)tgG>tgC	p.W884C	NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.W884C	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	884										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						GGCACTGGACCCAGTCCCTCC	0.577																																					p.W884C		.											.	.	0			c.G2652C						.						54.0	56.0	56.0					2																	133541732		1979	4160	6139	SO:0001583	missense	344148	exon14			CTGGACCCAGTCC	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.2652G>C	2.37:g.133541732C>G	ENSP00000387128:p.Trp884Cys	Somatic	174	0		WXS	Illumina HiSeq	Phase_I	85	52	NM_207363	0	0	0	0	0	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	c	11.53	1.664921	0.29604	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.10860	2.83;2.83	5.1	4.18	0.49190	.	0.226096	0.22876	U	0.054566	T	0.20820	0.0501	L	0.32530	0.975	0.58432	D	0.999998	D	0.89917	1.0	D	0.70935	0.971	T	0.00448	-1.1733	10	0.48119	T	0.1	.	13.5162	0.61541	0.1547:0.8453:0.0:0.0	.	884	O14513	NCKP5_HUMAN	C	884	ENSP00000387128:W884C;ENSP00000380603:W884C	ENSP00000380603:W884C	W	-	3	0	NCKAP5	133258202	0.911000	0.30947	0.557000	0.28306	0.216000	0.24613	3.191000	0.50981	2.661000	0.90470	0.651000	0.88453	TGG	.		0.577	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
TANC1	85461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	160084382	160084382	+	Missense_Mutation	SNP	T	T	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:160084382T>G	ENST00000263635.6	+	25	4193	c.3956T>G	c.(3955-3957)tTt>tGt	p.F1319C	TANC1_ENST00000454300.1_Missense_Mutation_p.F1213C	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1319					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						TTAAGAAAGTTTCCTCGAGAA	0.408																																					p.F1319C		.											.	TANC1-92	0			c.T3956G						.						82.0	84.0	83.0					2																	160084382		1871	4090	5961	SO:0001583	missense	85461	exon25			GAAAGTTTCCTCG	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.3956T>G	2.37:g.160084382T>G	ENSP00000263635:p.Phe1319Cys	Somatic	89	1		WXS	Illumina HiSeq	Phase_I	83	41	NM_033394	0	0	20	24	4	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.797780	0.90538	.	.	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.59083	0.29;0.29	6.07	6.07	0.98685	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.61324	0.2338	N	0.13043	0.29	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.979;0.964;0.996	T	0.61618	-0.7026	9	.	.	.	.	16.6288	0.85011	0.0:0.0:0.0:1.0	.	1311;1213;1319	B9EK39;Q9C0D5-2;Q9C0D5	.;.;TANC1_HUMAN	C	1213;1319	ENSP00000396339:F1213C;ENSP00000263635:F1319C	.	F	+	2	0	TANC1	159792628	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.040000	0.89188	2.326000	0.78906	0.533000	0.62120	TTT	.		0.408	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
ITM2C	81618	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	231741583	231741583	+	Silent	SNP	G	G	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:231741583G>C	ENST00000326427.6	+	4	588	c.462G>C	c.(460-462)gcG>gcC	p.A154A	ITM2C_ENST00000409704.2_Silent_p.A92A|ITM2C_ENST00000335005.6_Silent_p.A107A|ITM2C_ENST00000326407.6_Intron|ITM2C_ENST00000492029.1_3'UTR	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	154	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			cervix(2)|lung(1)|ovary(1)|skin(1)	5		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GTCTGACTGCGTACCATGATA	0.587																																					p.A154A		.											.	ITM2C-90	0			c.G462C						.						147.0	126.0	133.0					2																	231741583		2203	4300	6503	SO:0001819	synonymous_variant	81618	exon4			GACTGCGTACCAT	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"""BRICHOS domain containing"""	6175	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2C"""	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.462G>C	2.37:g.231741583G>C		Somatic	169	0		WXS	Illumina HiSeq	Phase_I	107	50	NM_030926	0	0	0	1	1	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Silent	SNP	ENST00000326427.6	37	CCDS2479.1																																																																																			.		0.587	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926	
DSN1	79980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	35399580	35399580	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr20:35399580C>A	ENST00000426836.1	-	3	423	c.51G>T	c.(49-51)atG>atT	p.M17I	DSN1_ENST00000373750.4_Missense_Mutation_p.M17I|DSN1_ENST00000373734.4_Intron|DSN1_ENST00000373740.3_Intron|DSN1_ENST00000373745.3_Missense_Mutation_p.M17I|DSN1_ENST00000448110.2_Start_Codon_SNP_p.M1I|DSN1_ENST00000473615.1_5'UTR	NM_001145316.1	NP_001138788.1	Q9H410	DSN1_HUMAN	DSN1, MIS12 kinetochore complex component	17					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|MIS12/MIND type complex (GO:0000444)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	16		Myeloproliferative disorder(115;0.00874)				GAGTCTTAGACATCACTGGTC	0.378																																					p.M17I		.											.	DSN1-92	0			c.G51T						.						110.0	110.0	110.0					20																	35399580		2203	4298	6501	SO:0001583	missense	79980	exon3			CTTAGACATCACT	AK023408	CCDS13286.1, CCDS46596.1, CCDS46597.1	20q11.23	2013-07-03	2013-07-03	2006-11-07	ENSG00000149636	ENSG00000149636			16165	protein-coding gene	gene with protein product	"""kinetochore null 3 homolog (C. elegans)"""	609175	"""chromosome 20 open reading frame 172"", ""DSN1, MIND kinetochore complex component, homolog (S. cerevisiae)"""	C20orf172		16585270, 20819937	Standard	NM_001145315		Approved	dJ469A13.2, MIS13, KNL3, hKNL-3	uc002xfz.3	Q9H410	OTTHUMG00000032396	ENST00000426836.1:c.51G>T	20.37:g.35399580C>A	ENSP00000389810:p.Met17Ile	Somatic	231	1		WXS	Illumina HiSeq	Phase_I	314	100	NM_001145315	0	0	6	11	5	B4DWT2|E1P5U9|Q5JW55|Q5JW56|Q9H8P4	Missense_Mutation	SNP	ENST00000426836.1	37	CCDS13286.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077408	0.36662	.	.	ENSG00000149636	ENST00000426836;ENST00000373745;ENST00000448110;ENST00000373750;ENST00000449595;ENST00000447406	.	.	.	4.97	0.0673	0.14365	.	0.921783	0.09213	N	0.833021	T	0.38639	0.1048	N	0.24115	0.695	0.80722	D	1	B	0.19331	0.035	B	0.17433	0.018	T	0.17258	-1.0375	9	0.33940	T	0.23	1.3087	5.4683	0.16656	0.1659:0.6997:0.0:0.1344	.	17	Q9H410	DSN1_HUMAN	I	17;17;1;17;1;17	.	ENSP00000362850:M17I	M	-	3	0	DSN1	34832994	0.384000	0.25164	0.863000	0.33907	0.951000	0.60555	-0.211000	0.09332	0.142000	0.18901	0.655000	0.94253	ATG	.		0.378	DSN1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079043.2	NM_024918	
NF2	4771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	30051666	30051666	+	Splice_Site	SNP	G	G	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr22:30051666G>A	ENST00000338641.4	+	6	1040		c.e6+1		NF2_ENST00000361452.4_Splice_Site|NF2_ENST00000403999.3_Splice_Site|NF2_ENST00000353887.4_Splice_Site|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000413209.2_Intron|NF2_ENST00000361166.4_Splice_Site|NF2_ENST00000361676.4_Splice_Site|NF2_ENST00000347330.5_Intron|NF2_ENST00000334961.7_Splice_Site|NF2_ENST00000403435.1_Splice_Site	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)						actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(5)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						GCCGAGCCAGGTGAGGCCCAT	0.408			"""D, Mis, N, F, S, O"""		"""meningioma, acoustic neuroma, renal """	"""meningioma, acoustic neuroma"""			Neurofibromatosis, type 2																												.		.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2-4696	5	Unknown(5)	meninges(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)	c.599+1G>A	GRCh37	CS951487	NF2	S		.						83.0	87.0	85.0					22																	30051666		2203	4300	6503	SO:0001630	splice_region_variant	4771	exon6	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	AGCCAGGTGAGGC	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"""A-kinase anchor proteins"""	7773	protein-coding gene	gene with protein product	"""moesin-ezrin-radixin like"", ""schwannomin"""	607379	"""neurofibromin 2 (bilateral acoustic neuroma)"""			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.599+1G>A	22.37:g.30051666G>A		Somatic	91	0		WXS	Illumina HiSeq	Phase_I	42	37	NM_016418	0	0	0	0	0	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Splice_Site	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.954606	0.92726	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.036	0.92978	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF2	28381666	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.653000	0.98506	2.484000	0.83849	0.555000	0.69702	.	.		0.408	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	Intron
CCR2	729230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	46399085	46399085	+	Missense_Mutation	SNP	T	T	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:46399085T>A	ENST00000400888.2	+	1	106	c.67T>A	c.(67-69)Ttt>Att	p.F23I	CCR2_ENST00000445132.2_Missense_Mutation_p.F23I|CCR2_ENST00000292301.4_Missense_Mutation_p.F23I|CCR2_ENST00000465202.1_Intron			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	23					blood vessel remodeling (GO:0001974)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular homeostasis (GO:0019725)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JAK-STAT cascade (GO:0007259)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of angiogenesis (GO:0016525)|negative regulation of eosinophil degranulation (GO:0043310)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of astrocyte chemotaxis (GO:2000464)|positive regulation of CD8-positive, alpha-beta T cell extravasation (GO:2000451)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of monocyte extravasation (GO:2000439)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of vascular endothelial growth factor production (GO:0010574)|response to wounding (GO:0009611)|T-helper 17 cell chemotaxis (GO:0035705)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|CCR2 chemokine receptor binding (GO:0031727)|chemokine receptor activity (GO:0004950)|protein homodimerization activity (GO:0042803)			breast(3)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)	14				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)		AGTCACCACCTTTTTTGATTA	0.478																																					p.F23I		.											.	CCR2-568	0			c.T67A						.						195.0	172.0	179.0					3																	46399085		1568	3582	5150	SO:0001583	missense	729230	exon2			ACCACCTTTTTTG		CCDS43078.1, CCDS46813.1	3p21	2012-08-08			ENSG00000121807	ENSG00000121807		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1603	protein-coding gene	gene with protein product		601267		CMKBR2		8146186	Standard	NM_001123041		Approved	CC-CKR-2, CKR2, MCP-1-R, CD192, FLJ78302	uc003cpn.4	P41597	OTTHUMG00000156466	ENST00000400888.2:c.67T>A	3.37:g.46399085T>A	ENSP00000383681:p.Phe23Ile	Somatic	280	1		WXS	Illumina HiSeq	Phase_I	280	136	NM_001123041	0	0	1	1	0	A0AVQ3|B2RMT0|Q4VBL2	Missense_Mutation	SNP	ENST00000400888.2	37	CCDS43078.1	.	.	.	.	.	.	.	.	.	.	T	9.930	1.214490	0.22289	.	.	ENSG00000121807	ENST00000445132;ENST00000292301;ENST00000421659;ENST00000400888	T;T;T;T	0.68479	-0.33;-0.31;1.34;-0.31	4.62	-6.25	0.02039	.	6.783580	0.00397	N	0.000040	T	0.40743	0.1129	N	0.12746	0.255	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15235	-1.0444	10	0.22109	T	0.4	.	2.8484	0.05550	0.3386:0.2093:0.3514:0.1007	.	23;23	P41597;Q4VBL2	CCR2_HUMAN;.	I	23	ENSP00000399285:F23I;ENSP00000292301:F23I;ENSP00000396736:F23I;ENSP00000383681:F23I	ENSP00000292301:F23I	F	+	1	0	CCR2	46374089	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	0.134000	0.15932	-0.799000	0.04439	-1.318000	0.01297	TTT	.		0.478	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647	
SLC26A6	65010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	48668741	48668741	+	Splice_Site	SNP	T	T	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:48668741T>C	ENST00000395550.2	-	8	951		c.e8-2		SLC26A6_ENST00000420764.2_Splice_Site|SLC26A6_ENST00000455886.2_Splice_Site|SLC26A6_ENST00000358747.6_Splice_Site|SLC26A6_ENST00000337000.8_Splice_Site|SLC26A6_ENST00000482282.1_5'Flank|SLC26A6_ENST00000383733.3_Splice_Site			Q9BXS9	S26A6_HUMAN	solute carrier family 26 (anion exchanger), member 6						angiotensin-activated signaling pathway (GO:0038166)|anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular response to cAMP (GO:0071320)|cellular response to fructose stimulus (GO:0071332)|cellular response to interferon-gamma (GO:0071346)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|epithelial fluid transport (GO:0042045)|formate transport (GO:0015724)|intestinal absorption (GO:0050892)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|mannitol transport (GO:0015797)|oxalate transport (GO:0019532)|oxalic acid secretion (GO:0046724)|positive regulation of dipeptide transmembrane transport (GO:2001150)|protein kinase C signaling (GO:0070528)|regulation of intracellular pH (GO:0051453)|sperm capacitation (GO:0048240)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transepithelial chloride transport (GO:0030321)|transepithelial transport (GO:0070633)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|chloride channel complex (GO:0034707)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle membrane (GO:0012506)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|chloride transmembrane transporter activity (GO:0015108)|efflux transmembrane transporter activity (GO:0015562)|formate efflux transmembrane transporter activity (GO:0015660)|formate transmembrane transporter activity (GO:0015499)|formate uptake transmembrane transporter activity (GO:0015659)|oxalate transmembrane transporter activity (GO:0019531)|PDZ domain binding (GO:0030165)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)		SLC26A6/PRKAR2A(2)	NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		CCCGATGAGCTGTGGGAGAGG	0.577																																					.	NSCLC(13;369 479 28271 30152 44026)	.											.	SLC26A6-946	0			c.841-2A>G						.						40.0	42.0	41.0					3																	48668741		2105	4230	6335	SO:0001630	splice_region_variant	65010	exon8			ATGAGCTGTGGGA	AF279265	CCDS43087.1, CCDS46824.1, CCDS46825.1, CCDS46826.1, CCDS63627.1, CCDS63628.1	3p21.31	2013-08-05	2013-07-18		ENSG00000225697	ENSG00000225697		"""Solute carriers"""	14472	protein-coding gene	gene with protein product	"""pendrin-like protein 1"", ""pendrin L1"", ""sulfate anion transporter"", ""anion transporter 1"""	610068	"""solute carrier family 26, member 6"""			11087667, 11247665	Standard	NM_022911		Approved	DKFZp586E1422		Q9BXS9	OTTHUMG00000186381	ENST00000395550.2:c.904-2A>G	3.37:g.48668741T>C		Somatic	24	0		WXS	Illumina HiSeq	Phase_I	13	8	NM_001040454	0	0	0	1	1	B4DMZ1|Q548A7|Q96Q90|Q9NQU1	Splice_Site	SNP	ENST00000395550.2	37	CCDS43087.1	.	.	.	.	.	.	.	.	.	.	T	19.71	3.878586	0.72294	.	.	ENSG00000225697	ENST00000420764;ENST00000395550;ENST00000383733;ENST00000337000;ENST00000447978;ENST00000358747;ENST00000455886;ENST00000421649	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9886	0.80183	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC26A6	48643745	1.000000	0.71417	0.988000	0.46212	0.877000	0.50540	7.298000	0.78815	2.173000	0.68751	0.533000	0.62120	.	.		0.577	SLC26A6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345040.1	NM_022911	Intron
RHOA	387	ucsc.edu	37	3	49394910	49394910	+	IGR	SNP	G	G	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:49394910G>A	ENST00000418115.1	-	0	2031				GPX1_ENST00000419349.1_3'UTR|GPX1_ENST00000419783.1_Missense_Mutation_p.P175S|GPX1_ENST00000496791.1_5'Flank	NM_001664.2	NP_001655.1	P61586	RHOA_HUMAN	ras homolog family member A						actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|apical junction assembly (GO:0043297)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cerebral cortex cell migration (GO:0021795)|cleavage furrow formation (GO:0036089)|forebrain radial glial cell differentiation (GO:0021861)|negative chemotaxis (GO:0050919)|negative regulation of axonogenesis (GO:0050771)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification involved in bone maturation (GO:0043931)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of podosome assembly (GO:0071803)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of translation (GO:0045727)|positive regulation of vasoconstriction (GO:0045907)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion transport (GO:0051924)|regulation of cell migration (GO:0030334)|regulation of dendrite development (GO:0050773)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of osteoblast proliferation (GO:0033688)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|Rho protein signal transduction (GO:0007266)|skeletal muscle tissue development (GO:0007519)|small GTPase mediated signal transduction (GO:0007264)|spindle assembly involved in mitosis (GO:0090307)|stress fiber assembly (GO:0043149)|stress-activated protein kinase signaling cascade (GO:0031098)|substantia nigra development (GO:0021762)|trabecula morphogenesis (GO:0061383)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	apical junction complex (GO:0043296)|axon (GO:0030424)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin binding (GO:0017022)			cervix(1)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CTGCGTAGGGGCACACCGTCA	0.622																																					.													.	GPX1-68	0			.						.						26.0	29.0	28.0					3																	49394910		1945	4124	6069	SO:0001628	intergenic_variant	2876	.			GTAGGGGCACACC	BC001360	CCDS2795.1	3p21.3	2012-02-27	2012-02-27	2004-03-23	ENSG00000067560	ENSG00000067560			667	protein-coding gene	gene with protein product		165390	"""ras homolog gene family, member A"""	ARH12, ARHA		9605859	Standard	NM_001664		Approved	RhoA, Rho12, RHOH12	uc003cwu.3	P61586	OTTHUMG00000156838		3.37:g.49394910G>A		Somatic	107	0		WXS	Illumina HiSeq		45	4	.	0	0	644	645	1	P06749|Q53HM4|Q5U024|Q9UDJ0|Q9UEJ4	Missense_Mutation	SNP	ENST00000418115.1	37	CCDS2795.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.847140	0.71603	.	.	ENSG00000233276	ENST00000419783	T	0.04049	3.72	5.4	5.4	0.78164	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.25568	0.0622	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00956	-1.1501	10	0.72032	D	0.01	.	17.761	0.88464	0.0:0.0:1.0:0.0	.	175	P07203	GPX1_HUMAN	S	175	ENSP00000407375:P175S	ENSP00000407375:P175S	P	-	1	0	GPX1	49369914	1.000000	0.71417	0.044000	0.18714	0.110000	0.19582	7.861000	0.87004	2.532000	0.85374	0.561000	0.74099	CCC	.		0.622	RHOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346157.3	NM_001664	
ZMYND10	51364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	50379017	50379017	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:50379017C>T	ENST00000231749.3	-	11	2507	c.1235G>A	c.(1234-1236)tGg>tAg	p.W412*	ZMYND10-AS1_ENST00000440013.1_RNA|RASSF1_ENST00000357043.2_5'Flank|ZMYND10_ENST00000360165.3_Nonsense_Mutation_p.W407*|RASSF1_ENST00000359365.4_5'Flank|ZMYND10_ENST00000490675.1_5'UTR|RASSF1_ENST00000488024.1_5'Flank	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	412	Interaction with LRRC6.				inner dynein arm assembly (GO:0036159)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)	centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|urinary_tract(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GCAGCAATACCACTCATTCTG	0.572										TSP Lung(30;0.18)																											p.W412X		.											.	ZMYND10-279	0			c.G1235A						.						138.0	129.0	132.0					3																	50379017		2203	4300	6503	SO:0001587	stop_gained	51364	exon11			CAATACCACTCAT	U70824	CCDS2825.1	3p21.3	2014-02-03			ENSG00000004838	ENSG00000004838		"""Zinc fingers, MYND-type"""	19412	protein-coding gene	gene with protein product		607070				12629521, 23891469	Standard	NM_015896		Approved	BLU, CILD22	uc003dag.1	O75800	OTTHUMG00000156874	ENST00000231749.3:c.1235G>A	3.37:g.50379017C>T	ENSP00000231749:p.Trp412*	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	78	30	NM_015896	0	0	0	0	0	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Nonsense_Mutation	SNP	ENST00000231749.3	37	CCDS2825.1	.	.	.	.	.	.	.	.	.	.	C	37	6.249939	0.97412	.	.	ENSG00000004838	ENST00000231749;ENST00000360165	.	.	.	5.4	5.4	0.78164	.	0.053779	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.9405	19.525	0.95201	0.0:1.0:0.0:0.0	.	.	.	.	X	412;407	.	ENSP00000231749:W412X	W	-	2	0	ZMYND10	50354021	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	7.761000	0.85260	2.699000	0.92147	0.655000	0.94253	TGG	.		0.572	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896	
FAM208A	23272	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	56658883	56658883	+	Missense_Mutation	SNP	G	G	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:56658883G>C	ENST00000493960.2	-	22	4301	c.4291C>G	c.(4291-4293)Cag>Gag	p.Q1431E	FAM208A_ENST00000431842.2_Missense_Mutation_p.Q994E|FAM208A_ENST00000485156.1_Intron|FAM208A_ENST00000355628.5_Missense_Mutation_p.Q1370E	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1431							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						TGTCGTTGCTGTATGTTCTGA	0.383																																					p.Q1431E		.											.	.	0			c.C4291G						.						127.0	125.0	126.0					3																	56658883		2203	4300	6503	SO:0001583	missense	23272	exon22			GTTGCTGTATGTT	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.4291C>G	3.37:g.56658883G>C	ENSP00000417509:p.Gln1431Glu	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	147	58	NM_001112736	0	0	14	28	14	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.279138	0.80692	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.53206	0.63;0.63;0.63	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000008	T	0.52613	0.1745	L	0.38838	1.175	0.47245	D	0.999367	P;B;D;B	0.61697	0.629;0.045;0.99;0.435	B;B;P;B	0.55011	0.382;0.094;0.766;0.104	T	0.54070	-0.8348	10	0.72032	D	0.01	-0.4466	14.6453	0.68756	0.0:0.0:0.8544:0.1456	.	1431;1370;994;1431	Q9UK61-3;Q9UK61-4;Q9UK61-2;Q9UK61	.;.;.;F208A_HUMAN	E	994;1431;1370	ENSP00000399410:Q994E;ENSP00000417509:Q1431E;ENSP00000347845:Q1370E	ENSP00000347845:Q1370E	Q	-	1	0	C3orf63	56633923	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.500000	0.81588	2.685000	0.91497	0.655000	0.94253	CAG	.		0.383	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
ACOX2	8309	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	58517532	58517532	+	Silent	SNP	C	C	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:58517532C>A	ENST00000302819.5	-	6	882	c.591G>T	c.(589-591)cgG>cgT	p.R197R	ACOX2_ENST00000459701.2_Silent_p.R197R	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	197					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		GGGTGGCTGACCGTCCCACTG	0.612																																					p.R197R		.											.	ACOX2-90	0			c.G591T						.						57.0	50.0	52.0					3																	58517532		2203	4300	6503	SO:0001819	synonymous_variant	8309	exon6			GGCTGACCGTCCC	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"""trihydroxycoprostanoyl-CoA oxidase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"""	601641	"""acyl-Coenzyme A oxidase 2, branched chain"""			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.591G>T	3.37:g.58517532C>A		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	34	18	NM_003500	0	0	0	0	0	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	37	CCDS33775.1																																																																																			.		0.612	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
ZBTB11	27107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	101370105	101370105	+	Missense_Mutation	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:101370105C>T	ENST00000312938.4	-	11	3647	c.3067G>A	c.(3067-3069)Gta>Ata	p.V1023I		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	1023					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TGTGCTAATACATAATTAACC	0.398																																					p.V1023I		.											.	ZBTB11-91	0			c.G3067A						.						135.0	131.0	132.0					3																	101370105		2203	4300	6503	SO:0001583	missense	27107	exon11			CTAATACATAATT	U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.3067G>A	3.37:g.101370105C>T	ENSP00000326200:p.Val1023Ile	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	168	70	NM_014415	0	0	6	15	9	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	37	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.982094	0.93044	.	.	ENSG00000066422	ENST00000312938	T	0.12672	2.66	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.28300	0.0699	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.00899	-1.1522	10	0.30078	T	0.28	-12.9426	19.5182	0.95174	0.0:1.0:0.0:0.0	.	1023	O95625	ZBT11_HUMAN	I	1023	ENSP00000326200:V1023I	ENSP00000326200:V1023I	V	-	1	0	ZBTB11	102852795	1.000000	0.71417	0.987000	0.45799	0.985000	0.73830	7.445000	0.80570	2.692000	0.91855	0.555000	0.69702	GTA	.		0.398	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415	
KIAA2018	205717	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	113376409	113376409	+	Missense_Mutation	SNP	T	T	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:113376409T>C	ENST00000478658.1	-	5	4137	c.4120A>G	c.(4120-4122)Atg>Gtg	p.M1374V	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Missense_Mutation_p.M1374V			Q68DE3	K2018_HUMAN	KIAA2018	1374						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						TGACTGACCATCATTTGAGTT	0.468																																					p.M1374V		.											.	KIAA2018-93	0			c.A4120G						.						105.0	102.0	103.0					3																	113376409		1991	4160	6151	SO:0001583	missense	205717	exon7			TGACCATCATTTG	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4120A>G	3.37:g.113376409T>C	ENSP00000420721:p.Met1374Val	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	96	38	NM_001009899	0	0	2	2	0	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	T	10.68	1.417459	0.25552	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.18338	2.22;2.22	5.68	4.46	0.54185	.	0.087940	0.85682	D	0.000000	T	0.13415	0.0325	L	0.32530	0.975	0.47862	D	0.999537	B	0.30406	0.278	B	0.30179	0.112	T	0.07404	-1.0774	10	0.37606	T	0.19	-12.1634	11.116	0.48259	0.0:0.0:0.3371:0.6629	.	1374	Q68DE3	K2018_HUMAN	V	1374	ENSP00000320794:M1374V;ENSP00000420721:M1374V	ENSP00000320794:M1374V	M	-	1	0	KIAA2018	114859099	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	2.543000	0.45752	2.169000	0.68431	0.402000	0.26972	ATG	.		0.468	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
FSTL1	11167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	120122159	120122159	+	Silent	SNP	A	A	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:120122159A>G	ENST00000295633.3	-	8	980	c.624T>C	c.(622-624)aaT>aaC	p.N208N	FSTL1_ENST00000424703.2_Silent_p.N173N	NM_007085.4	NP_009016.1	Q12841	FSTL1_HUMAN	follistatin-like 1	208	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				BMP signaling pathway (GO:0030509)|response to starvation (GO:0042594)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|skin(1)	20				GBM - Glioblastoma multiforme(114;0.189)		TCCAATCAGCATTTTCATCAG	0.438																																					p.N208N		.											.	FSTL1-90	0			c.T624C						.						106.0	106.0	106.0					3																	120122159		2203	4300	6503	SO:0001819	synonymous_variant	11167	exon8			ATCAGCATTTTCA	U06863	CCDS2998.1	3q13.33	2013-01-10			ENSG00000163430	ENSG00000163430		"""EF-hand domain containing"""	3972	protein-coding gene	gene with protein product		605547				7957230, 9786430	Standard	NM_007085		Approved	FRP, FSL1	uc003eds.3	Q12841	OTTHUMG00000159440	ENST00000295633.3:c.624T>C	3.37:g.120122159A>G		Somatic	132	0		WXS	Illumina HiSeq	Phase_I	156	65	NM_007085	0	0	91	181	90	A8K523|B4DTT5|D3DN90|Q549Z0	Silent	SNP	ENST00000295633.3	37	CCDS2998.1																																																																																			.		0.438	FSTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355399.1	NM_007085	
ETV5	2119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	185766603	185766603	+	Missense_Mutation	SNP	G	G	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:185766603G>A	ENST00000306376.5	-	13	1604	c.1358C>T	c.(1357-1359)gCc>gTc	p.A453V	ETV5_ENST00000434744.1_Missense_Mutation_p.A453V|ETV5_ENST00000537818.1_Missense_Mutation_p.A495V|ETV5_ENST00000480706.1_5'UTR	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	453					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			GGAGAAGAGGGCATCTGGGTC	0.582			T	"""TMPRSS2, SCL45A3"""	Prostate																																p.A453V		.		Dom	yes		3	3q28	2119	ets variant gene 5		E	.	ETV5-706	0			c.C1358T						.						70.0	61.0	64.0					3																	185766603		2203	4300	6503	SO:0001583	missense	2119	exon13			AAGAGGGCATCTG	BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"""ets-related molecule"""	601600	"""ets variant gene 5 (ets-related molecule)"""			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.1358C>T	3.37:g.185766603G>A	ENSP00000306894:p.Ala453Val	Somatic	73	0		WXS	Illumina HiSeq	Phase_I	43	25	NM_004454	0	0	7	8	1	A6NH46|B7Z7D7|Q6IBN5	Missense_Mutation	SNP	ENST00000306376.5	37	CCDS33906.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.043894	0.93685	.	.	ENSG00000244405	ENST00000306376;ENST00000434744;ENST00000537818	T;T;T	0.54866	0.55;0.55;0.55	5.85	5.85	0.93711	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.69548	0.3123	L	0.49513	1.565	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.70149	-0.4951	10	0.87932	D	0	.	18.9349	0.92582	0.0:0.0:1.0:0.0	.	453;495	P41161;B7Z7D7	ETV5_HUMAN;.	V	453;453;495	ENSP00000306894:A453V;ENSP00000413755:A453V;ENSP00000441737:A495V	ENSP00000306894:A453V	A	-	2	0	ETV5	187249297	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.773000	0.95371	0.655000	0.94253	GCC	.		0.582	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454	
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	187539870	187539870	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr4:187539870C>A	ENST00000441802.2	-	10	8079	c.7870G>T	c.(7870-7872)Gat>Tat	p.D2624Y		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2624	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GAGCCCTCATCGGCATCACTT	0.443										HNSCC(5;0.00058)																											p.D2624Y	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.G7870T						.						63.0	59.0	60.0					4																	187539870		1948	4127	6075	SO:0001583	missense	2195	exon10			CCTCATCGGCATC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.7870G>T	4.37:g.187539870C>A	ENSP00000406229:p.Asp2624Tyr	Somatic	79	0		WXS	Illumina HiSeq	Phase_I	84	37	NM_005245	0	0	30	75	45		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612696	0.46631	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.74737	-0.87	5.2	5.2	0.72013	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.92675	0.7672	H	0.99090	4.425	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95297	0.8400	10	0.87932	D	0	.	19.2916	0.94102	0.0:1.0:0.0:0.0	.	2624	Q14517	FAT1_HUMAN	Y	2624;2626	ENSP00000406229:D2624Y	ENSP00000260147:D2626Y	D	-	1	0	FAT1	187776864	1.000000	0.71417	0.347000	0.25668	0.077000	0.17291	7.651000	0.83577	2.861000	0.98227	0.655000	0.94253	GAT	.		0.443	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
CLPTM1L	81037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	1335258	1335258	+	Missense_Mutation	SNP	A	A	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr5:1335258A>G	ENST00000320895.5	-	6	967	c.710T>C	c.(709-711)cTc>cCc	p.L237P	CLPTM1L_ENST00000507807.1_Missense_Mutation_p.L104P|CLPTM1L_ENST00000320927.6_Missense_Mutation_p.L237P	NM_030782.3	NP_110409.2	Q96KA5	CLP1L_HUMAN	CLPTM1-like	237					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		GGACACGGTGAGGGGCAGCTC	0.627																																					p.L237P		.											.	CLPTM1L-153	0			c.T710C						.						109.0	103.0	105.0					5																	1335258		2203	4300	6503	SO:0001583	missense	81037	exon6			ACGGTGAGGGGCA	AK027306	CCDS3862.1	5p15.33	2008-02-05			ENSG00000049656	ENSG00000049656			24308	protein-coding gene	gene with protein product	"""cisplatin resistance related protein"""	612585				11162647	Standard	NM_030782		Approved	FLJ14400, CRR9	uc003jch.3	Q96KA5	OTTHUMG00000131015	ENST00000320895.5:c.710T>C	5.37:g.1335258A>G	ENSP00000313854:p.Leu237Pro	Somatic	197	1		WXS	Illumina HiSeq	Phase_I	88	32	NM_030782	0	0	46	84	38	D3DTC1|Q658W6|Q7LG29|Q96AZ0|Q9H3N4	Missense_Mutation	SNP	ENST00000320895.5	37	CCDS3862.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.137656	0.77775	.	.	ENSG00000049656	ENST00000320895;ENST00000507807;ENST00000320927	T;T;T	0.63580	0.08;0.06;-0.05	4.41	4.41	0.53225	.	0.062767	0.64402	D	0.000003	T	0.81327	0.4799	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.991	D	0.85481	0.1179	10	0.87932	D	0	-41.3822	13.952	0.64123	1.0:0.0:0.0:0.0	.	237;104	Q96KA5;G5E9Z2	CLP1L_HUMAN;.	P	237;104;237	ENSP00000313854:L237P;ENSP00000423321:L104P;ENSP00000315196:L237P	ENSP00000313854:L237P	L	-	2	0	CLPTM1L	1388258	1.000000	0.71417	0.954000	0.39281	0.935000	0.57460	8.653000	0.91088	1.735000	0.51646	0.523000	0.50628	CTC	.		0.627	CLPTM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253649.2	NM_030782	
HLA-G	3135	ucsc.edu	37	6	29797394	29797394	+	Silent	SNP	G	G	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr6:29797394G>A	ENST00000360323.6	+	4	843	c.819G>A	c.(817-819)gtG>gtA	p.V273V	HLA-G_ENST00000428701.1_Silent_p.V273V|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376828.2_Silent_p.V278V|HLA-G_ENST00000376818.3_Silent_p.V181V			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	273	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CTGTGGTGGTGCCTTCTGGAG	0.627																																					p.V273V													.	HLA-G-517	0			c.G819A						.						63.0	58.0	60.0					6																	29797394		2203	4296	6499	SO:0001819	synonymous_variant	3135	exon5			GGTGGTGCCTTCT		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.819G>A	6.37:g.29797394G>A		Somatic	191	0		WXS	Illumina HiSeq		61	1	NM_002127	21	6	379	3352	2943		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			.		0.627	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
AKAP12	9590	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	151626981	151626981	+	Missense_Mutation	SNP	C	C	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr6:151626981C>G	ENST00000253332.1	+	2	451	c.262C>G	c.(262-264)Ctg>Gtg	p.L88V	AKAP12_ENST00000402676.2_Missense_Mutation_p.L88V			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	88					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GAAAGGAGCCCTGAACGGTCA	0.552																																					p.L88V	Melanoma(141;1616 1805 10049 24534 51979)	.											.	AKAP12-293	0			c.C262G						.						53.0	46.0	49.0					6																	151626981		2203	4300	6503	SO:0001583	missense	9590	exon3			GGAGCCCTGAACG	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"""A-kinase anchor proteins"""	370	protein-coding gene	gene with protein product	"""gravin"", ""Src-Suppressed C Kinase Substrate"""	604698	"""A kinase (PRKA) anchor protein (gravin) 12"""			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.262C>G	6.37:g.151626981C>G	ENSP00000253332:p.Leu88Val	Somatic	48	0		WXS	Illumina HiSeq	Phase_I	34	13	NM_005100	0	0	12	21	9	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	C	0.285	-0.983780	0.02180	.	.	ENSG00000131016	ENST00000402676;ENST00000253332	T;T	0.08546	3.08;3.08	0.158	0.158	0.14942	.	.	.	.	.	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.48031	-0.9070	8	0.30854	T	0.27	.	.	.	.	.	88	Q02952	AKA12_HUMAN	V	88	ENSP00000384537:L88V;ENSP00000253332:L88V	ENSP00000253332:L88V	L	+	1	2	AKAP12	151668674	.	.	0.029000	0.17559	0.052000	0.14988	.	.	0.202000	0.20498	0.205000	0.17691	CTG	.		0.552	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
PGAM2	5224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	44105125	44105125	+	Missense_Mutation	SNP	C	C	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr7:44105125C>A	ENST00000297283.3	-	1	61	c.4G>T	c.(4-6)Gcc>Tcc	p.A2S	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	2					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)			large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						CGGTGAGTGGCCATGGTGGCA	0.607																																					p.A2S		.											.	PGAM2-226	0			c.G4T						.						62.0	54.0	57.0					7																	44105125		2203	4300	6503	SO:0001583	missense	5224	exon1			GAGTGGCCATGGT		CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.4G>T	7.37:g.44105125C>A	ENSP00000297283:p.Ala2Ser	Somatic	136	0		WXS	Illumina HiSeq	Phase_I	107	38	NM_000290	0	0	2	2	0		Missense_Mutation	SNP	ENST00000297283.3	37	CCDS34624.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.060303	0.36373	.	.	ENSG00000164708	ENST00000297283	T	0.80909	-1.43	5.93	-3.63	0.04529	.	0.487586	0.24258	N	0.040105	T	0.55162	0.1903	N	0.05554	-0.025	0.29035	N	0.885422	B	0.06786	0.001	B	0.10450	0.005	T	0.40979	-0.9534	10	0.45353	T	0.12	-11.1352	6.6092	0.22741	0.115:0.5762:0.2239:0.0848	.	2	P15259	PGAM2_HUMAN	S	2	ENSP00000297283:A2S	ENSP00000297283:A2S	A	-	1	0	PGAM2	44071650	0.648000	0.27313	0.979000	0.43373	0.986000	0.74619	-0.141000	0.10327	-0.536000	0.06298	0.650000	0.86243	GCC	.		0.607	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1		
TMED4	222068	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	44621125	44621125	+	Missense_Mutation	SNP	A	A	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr7:44621125A>G	ENST00000457408.2	-	3	362	c.310T>C	c.(310-312)Tcc>Ccc	p.S104P	TMED4_ENST00000289577.5_Missense_Mutation_p.S104P|TMED4_ENST00000444131.2_5'UTR|TMED4_ENST00000481238.1_Missense_Mutation_p.S104P	NM_182547.2	NP_872353.2	Q7Z7H5	TMED4_HUMAN	transmembrane emp24 protein transport domain containing 4	104	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6						GGCGTGTGGGAGGTGAACGTG	0.557																																					p.S104P		.											.	TMED4-90	0			c.T310C						.						89.0	89.0	89.0					7																	44621125		2203	4300	6503	SO:0001583	missense	222068	exon3			TGTGGGAGGTGAA	BC035467	CCDS5493.1	7p13	2004-12-21			ENSG00000158604	ENSG00000158604			22301	protein-coding gene	gene with protein product		612038				12761501	Standard	NM_182547		Approved	HNLF	uc003tli.3	Q7Z7H5	OTTHUMG00000129210	ENST00000457408.2:c.310T>C	7.37:g.44621125A>G	ENSP00000404042:p.Ser104Pro	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	76	41	NM_182547	0	0	79	144	65	A4D2K8|B4DFJ4|Q56VW3|Q7Z432|Q8N2P6	Missense_Mutation	SNP	ENST00000457408.2	37	CCDS5493.1	.	.	.	.	.	.	.	.	.	.	A	34	5.340815	0.95783	.	.	ENSG00000158604	ENST00000457408;ENST00000289577;ENST00000419520;ENST00000481238	T;T;T	0.18502	2.21;2.21;2.21	5.22	5.22	0.72569	GOLD (2);	0.000000	0.85682	D	0.000000	T	0.51007	0.1649	M	0.93720	3.45	0.80722	D	1	D;D	0.76494	0.999;0.984	D;D	0.74348	0.983;0.962	T	0.63795	-0.6556	10	0.87932	D	0	-13.0927	13.1033	0.59233	1.0:0.0:0.0:0.0	.	104;104	Q7Z7H5-3;Q7Z7H5	.;TMED4_HUMAN	P	104;104;88;104	ENSP00000404042:S104P;ENSP00000289577:S104P;ENSP00000417443:S104P	ENSP00000289577:S104P	S	-	1	0	TMED4	44587650	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.944000	0.92980	2.191000	0.70037	0.533000	0.62120	TCC	.		0.557	TMED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251290.1	NM_182547	
ADAM28	10863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	24209520	24209520	+	Silent	SNP	T	T	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:24209520T>C	ENST00000265769.4	+	21	2309	c.2199T>C	c.(2197-2199)caT>caC	p.H733H	RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000397649.3_Missense_Mutation_p.C482R|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	733					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TGAAGCCCCATGTGTATGATC	0.378																																					p.H733H	NSCLC(193;488 2149 22258 34798 40734)	.											.	ADAM28-228	0			c.T2199C						.						117.0	114.0	115.0					8																	24209520		2203	4300	6503	SO:0001819	synonymous_variant	10863	exon21			GCCCCATGTGTAT	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.2199T>C	8.37:g.24209520T>C		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	135	56	NM_014265	0	0	2	3	1	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	T	7.970	0.748895	0.15710	.	.	ENSG00000042980	ENST00000397649;ENST00000521629	T	0.01745	4.66	4.14	-4.67	0.03319	.	.	.	.	.	T	0.01800	0.0057	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.42189	-0.9466	6	0.87932	D	0	.	2.3577	0.04300	0.1532:0.4266:0.1567:0.2635	.	.	.	.	R	482;366	ENSP00000380770:C482R	ENSP00000380770:C482R	C	+	1	0	ADAM28	24265465	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.317000	0.01122	-0.875000	0.04022	-0.347000	0.07816	TGT	.		0.378	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
BNIP3L	665	hgsc.bcm.edu	37	8	26240664	26240664	+	Silent	SNP	C	C	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:26240664C>G	ENST00000380629.2	+	1	251	c.18C>G	c.(16-18)gtC>gtG	p.V6V	BNIP3L_ENST00000520409.1_5'Flank|BNIP3L_ENST00000523515.1_5'Flank|SDAD1P1_ENST00000519902.1_RNA	NM_004331.2	NP_004322.1	O60238	BNI3L_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 3-like	6					defense response to virus (GO:0051607)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrial protein catabolic process (GO:0035694)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			large_intestine(3)|lung(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0019)|Epithelial(17;1.59e-12)|all cancers(2;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(2;2.57e-08)|Colorectal(74;0.135)		CCCACCTAGTCGAGCCGCCGC	0.662																																					p.V6V		.											.	BNIP3L-227	0			c.C18G						.						16.0	19.0	18.0					8																	26240664		2177	4263	6440	SO:0001819	synonymous_variant	665	exon1			CCTAGTCGAGCCG	AB004788	CCDS6050.1	8p21	2014-05-13	2002-08-29		ENSG00000104765	ENSG00000104765			1085	protein-coding gene	gene with protein product		605368	"""BCL2/adenovirus E1B 19kD-interacting protein 3-like"""			9523198, 9973195	Standard	NM_004331		Approved	Nix, BNIP3a	uc003xex.1	O60238	OTTHUMG00000099433	ENST00000380629.2:c.18C>G	8.37:g.26240664C>G		Somatic	66	0		WXS	Illumina HiSeq	Phase_I	37	2	NM_004331	0	0	51	51	0	B0AZS9|Q5JW63|Q8NF87	Silent	SNP	ENST00000380629.2	37	CCDS6050.1																																																																																			.		0.662	BNIP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216895.1	NM_004331	
RAB11FIP1	80223	broad.mit.edu	37	8	37729419	37729419	+	Silent	SNP	C	C	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:37729419C>A	ENST00000330843.4	-	4	2913	c.2901G>T	c.(2899-2901)tcG>tcT	p.S967S	RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000523182.1_5'UTR|RAB11FIP1_ENST00000287263.4_Intron	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	967					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			TTTCATCATCCGATGCGACTT	0.453																																					p.S967S													.	RAB11FIP1-92	0			c.G2901T						.						156.0	128.0	137.0					8																	37729419		2203	4300	6503	SO:0001819	synonymous_variant	80223	exon4			ATCATCCGATGCG	AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.2901G>T	8.37:g.37729419C>A		Somatic	164	0		WXS	Illumina HiSeq	Phase_I	176	7	NM_001002814	0	0	4	4	0	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Silent	SNP	ENST00000330843.4	37	CCDS34882.1																																																																																			.		0.453	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151	
XKR4	114786	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	8	56435874	56435874	+	Silent	SNP	C	C	G	rs4263738		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:56435874C>G	ENST00000327381.6	+	3	1141	c.1041C>G	c.(1039-1041)gcC>gcG	p.A347A	RP11-628E19.2_ENST00000522918.1_RNA	NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	347						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			TGTCCCTGGCCTGGGCCTTGG	0.562																																					p.A347A		.											.	XKR4-92	0			c.C1041G						.						62.0	57.0	59.0					8																	56435874		2203	4300	6503	SO:0001819	synonymous_variant	114786	exon3			CCTGGCCTGGGCC	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 4"""				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.1041C>G	8.37:g.56435874C>G		Somatic	78	0		WXS	Illumina HiSeq	Phase_I	39	19	NM_052898	0	0	5	13	8	Q96PZ8	Silent	SNP	ENST00000327381.6	37	CCDS34893.1																																																																																			.		0.562	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898	
HNF4G	3174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	76465335	76465335	+	Missense_Mutation	SNP	T	T	C			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:76465335T>C	ENST00000354370.1	+	6	677	c.407T>C	c.(406-408)aTt>aCt	p.I136T	HNF4G_ENST00000396423.2_Missense_Mutation_p.I173T			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	136					endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	37	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			ATTGCAAGTATTGGTGATGTC	0.358																																					p.I173T		.											.	HNF4G-187	0			c.T518C						.						120.0	109.0	113.0					8																	76465335		2203	4300	6503	SO:0001583	missense	3174	exon5			CAAGTATTGGTGA		CCDS6220.2	8q21-q22	2013-01-16			ENSG00000164749	ENSG00000164749		"""Nuclear hormone receptors"""	5026	protein-coding gene	gene with protein product		605966				8622695, 12220494	Standard	NM_004133		Approved	NR2A2	uc003yar.3	Q14541	OTTHUMG00000149920	ENST00000354370.1:c.407T>C	8.37:g.76465335T>C	ENSP00000346339:p.Ile136Thr	Somatic	83	0		WXS	Illumina HiSeq	Phase_I	120	58	NM_004133	0	0	13	20	7	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	37		.	.	.	.	.	.	.	.	.	.	T	17.96	3.517111	0.64634	.	.	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.94723	-3.5;-3.5	5.4	5.4	0.78164	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.102401	0.64402	D	0.000003	D	0.93769	0.8008	M	0.71036	2.16	0.58432	D	0.999998	B;B	0.10296	0.001;0.003	B;B	0.21151	0.02;0.033	D	0.91547	0.5254	10	0.66056	D	0.02	.	15.5943	0.76566	0.0:0.0:0.0:1.0	.	173;136	F1D8Q4;Q14541	.;HNF4G_HUMAN	T	136;173	ENSP00000346339:I136T;ENSP00000379701:I173T	ENSP00000346339:I136T	I	+	2	0	HNF4G	76627890	1.000000	0.71417	0.985000	0.45067	0.994000	0.84299	7.450000	0.80656	2.263000	0.75096	0.533000	0.62120	ATT	.		0.358	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133	
PTK2	5747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	141745382	141745382	+	Silent	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:141745382C>T	ENST00000522684.1	-	22	2227	c.1998G>A	c.(1996-1998)cgG>cgA	p.R666R	PTK2_ENST00000340930.3_Silent_p.R666R|PTK2_ENST00000517887.1_Silent_p.R710R|PTK2_ENST00000538769.1_Silent_p.R334R|PTK2_ENST00000521059.1_Silent_p.R666R|PTK2_ENST00000535192.1_Silent_p.R666R|MIR151A_ENST00000521276.1_RNA|PTK2_ENST00000395218.2_Silent_p.R666R|PTK2_ENST00000519419.1_Silent_p.R710R|PTK2_ENST00000519465.1_Silent_p.R294R	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	666	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			TAAACCTGGGCCGCCTGCTGG	0.532																																					p.R688R		.											.	PTK2-1517	0			c.G2064A						.						61.0	52.0	55.0					8																	141745382		2203	4300	6503	SO:0001819	synonymous_variant	5747	exon22			CCTGGGCCGCCTG	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9611	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 71"""	600758	"""PTK2 protein tyrosine kinase 2"""			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.1998G>A	8.37:g.141745382C>T		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	29	15	NM_005607	0	1	25	56	30	B4E2N6|F5H4S4|Q14291|Q9UD85	Silent	SNP	ENST00000522684.1	37	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	C	9.232	1.036008	0.19590	.	.	ENSG00000169398	ENST00000519654	.	.	.	5.51	3.39	0.38822	.	.	.	.	.	T	0.62171	0.2406	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60591	-0.7233	4	.	.	.	.	11.6247	0.51138	0.0:0.7826:0.0:0.2174	.	.	.	.	T	677	.	.	A	-	1	0	PTK2	141814564	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.429000	0.34903	1.340000	0.45581	-0.136000	0.14681	GCC	.		0.532	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
TMEM261	90871	broad.mit.edu	37	9	7799724	7799724	+	Missense_Mutation	SNP	C	C	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr9:7799724C>G	ENST00000358227.4	-	1	343	c.11G>C	c.(10-12)cGg>cCg	p.R4P	TMEM261_ENST00000484082.1_Intron	NM_033428.1	NP_219500.1	Q96GE9	TM261_HUMAN	transmembrane protein 261	4						integral component of membrane (GO:0016021)											CTGGGACAACCGAGACCCCAT	0.642																																					p.R4P													.	C9orf123-90	0			c.G11C						.						24.0	23.0	23.0					9																	7799724		2203	4300	6503	SO:0001583	missense	90871	exon1			GACAACCGAGACC	BC009510	CCDS34989.1	9p24.1	2014-02-21	2013-09-11	2013-09-11	ENSG00000137038	ENSG00000137038			30536	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 123"""	C9orf123		21666724	Standard	NM_033428		Approved	MGC4730	uc003zkj.3	Q96GE9	OTTHUMG00000019539	ENST00000358227.4:c.11G>C	9.37:g.7799724C>G	ENSP00000350961:p.Arg4Pro	Somatic	53	0		WXS	Illumina HiSeq	Phase_I	35	4	NM_033428	0	0	84	84	0	A8K9B7|Q5T6Y9|Q9NT74	Missense_Mutation	SNP	ENST00000358227.4	37	CCDS34989.1	.	.	.	.	.	.	.	.	.	.	c	8.371	0.835299	0.16820	.	.	ENSG00000137038	ENST00000358227	T	0.44881	0.91	4.48	-8.96	0.00761	.	4.734690	0.00682	N	0.000688	T	0.19087	0.0458	N	0.08118	0	0.09310	N	1	B;B	0.26445	0.149;0.149	B;B	0.30316	0.114;0.114	T	0.12993	-1.0526	10	0.26408	T	0.33	-18.367	4.0438	0.09763	0.1403:0.0854:0.5667:0.2076	.	4;4	Q96GE9-2;Q96GE9	.;CI123_HUMAN	P	4	ENSP00000350961:R4P	ENSP00000350961:R4P	R	-	2	0	C9orf123	7789724	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.562000	0.00920	-2.210000	0.00738	-2.363000	0.00238	CGG	.		0.642	TMEM261-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051705.1	NM_033428	
SEC61B	10952	bcgsc.ca	37	9	101992685	101992685	+	Missense_Mutation	SNP	G	G	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr9:101992685G>T	ENST00000223641.4	+	4	333	c.270G>T	c.(268-270)tgG>tgT	p.W90C	SEC61B_ENST00000498603.1_Missense_Mutation_p.W36C	NM_006808.2	NP_006799.1	P60468	SC61B_HUMAN	Sec61 beta subunit	90					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|gene expression (GO:0010467)|protein import into nucleus, translocation (GO:0000060)|retrograde protein transport, ER to cytosol (GO:0030970)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum Sec complex (GO:0031205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	epidermal growth factor binding (GO:0048408)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			kidney(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(62;0.0559)				TGCACATTTGGGGCAAGTACA	0.388																																					p.W90C													.	SEC61B-90	0			c.G270T						.						273.0	251.0	258.0					9																	101992685		2203	4299	6502	SO:0001583	missense	10952	exon4			CATTTGGGGCAAG	L25085	CCDS6741.1	9q22.32-q31.3	2009-03-19			ENSG00000106803	ENSG00000106803			16993	protein-coding gene	gene with protein product		609214				8107851, 10212142	Standard	NM_006808		Approved		uc004azh.3	P60468	OTTHUMG00000020354	ENST00000223641.4:c.270G>T	9.37:g.101992685G>T	ENSP00000223641:p.Trp90Cys	Somatic	216	0		WXS	Illumina HiSeq	Phase_1	255	14	NM_006808	0	0	71	71	0	P38390|P38391|Q6IBC1	Missense_Mutation	SNP	ENST00000223641.4	37	CCDS6741.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.528131	0.85706	.	.	ENSG00000106803	ENST00000223641	.	.	.	5.83	5.83	0.93111	.	0.126644	0.56097	D	0.000021	D	0.83041	0.5168	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.83390	0.0017	8	0.59425	D	0.04	.	19.7125	0.96102	0.0:0.0:1.0:0.0	.	90	P60468	SC61B_HUMAN	C	90	.	ENSP00000223641:W90C	W	+	3	0	SEC61B	101032506	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.242000	0.95408	2.767000	0.95098	0.650000	0.86243	TGG	.		0.388	SEC61B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053391.1	NM_006808	
TBC1D13	54662	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	131565636	131565636	+	Missense_Mutation	SNP	C	C	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr9:131565636C>G	ENST00000372648.5	+	8	801	c.651C>G	c.(649-651)atC>atG	p.I217M	TBC1D13_ENST00000539497.1_Missense_Mutation_p.I36M|TBC1D13_ENST00000466056.1_3'UTR|TBC1D13_ENST00000223865.8_Intron	NM_018201.3	NP_060671.3	Q9NVG8	TBC13_HUMAN	TBC1 domain family, member 13	217	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	6						TCCTGTTCATCTACGCCAAGC	0.552																																					p.I217M		.											.	TBC1D13-90	0			c.C651G						.						151.0	121.0	131.0					9																	131565636		2203	4300	6503	SO:0001583	missense	54662	exon8			GTTCATCTACGCC	AK001605	CCDS6911.1, CCDS69677.1	9q34.13	2013-07-09			ENSG00000107021	ENSG00000107021			25571	protein-coding gene	gene with protein product						22762500	Standard	XM_005252060		Approved	FLJ10743	uc010myj.3	Q9NVG8	OTTHUMG00000020760	ENST00000372648.5:c.651C>G	9.37:g.131565636C>G	ENSP00000361731:p.Ile217Met	Somatic	109	0		WXS	Illumina HiSeq	Phase_I	65	34	NM_018201	0	0	16	30	14	A7E2E7|B3KW04|B9EGJ8|Q5T270|Q5T271	Missense_Mutation	SNP	ENST00000372648.5	37	CCDS6911.1	.	.	.	.	.	.	.	.	.	.	C	19.71	3.879150	0.72294	.	.	ENSG00000107021	ENST00000372648;ENST00000539497	T;T	0.12569	2.67;2.67	5.48	4.56	0.56223	Rab-GAP/TBC domain (4);	0.111120	0.64402	N	0.000011	T	0.29976	0.0750	M	0.78223	2.4	0.80722	D	1	D	0.55605	0.972	P	0.58721	0.844	T	0.02588	-1.1137	10	0.41790	T	0.15	-25.7081	8.7782	0.34776	0.0:0.769:0.1524:0.0786	.	217	Q9NVG8	TBC13_HUMAN	M	217;36	ENSP00000361731:I217M;ENSP00000437751:I36M	ENSP00000361731:I217M	I	+	3	3	TBC1D13	130605457	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	4.786000	0.62425	1.253000	0.44018	0.655000	0.94253	ATC	.		0.552	TBC1D13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054496.1	NM_018201	
NXF3	56000	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	102337711	102337711	+	Missense_Mutation	SNP	C	C	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chrX:102337711C>T	ENST00000395065.3	-	8	858	c.757G>A	c.(757-759)Gtc>Atc	p.V253I	NXF3_ENST00000425463.2_Missense_Mutation_p.V164I|NXF3_ENST00000425644.1_5'UTR	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	253					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)			NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						TCTTCATGGACGTCCAGGGAG	0.478																																					p.V253I		.											.	NXF3-205	0			c.G757A						.						174.0	145.0	154.0					X																	102337711		2203	4300	6503	SO:0001583	missense	56000	exon8			CATGGACGTCCAG	AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.757G>A	X.37:g.102337711C>T	ENSP00000378504:p.Val253Ile	Somatic	155	1		WXS	Illumina HiSeq	Phase_I	91	87	NM_022052	0	0	0	0	0	B4DYS7|Q5H9I1|Q9H1A9	Missense_Mutation	SNP	ENST00000395065.3	37	CCDS14503.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.019|0.019	-1.461864|-1.461864	0.01062|0.01062	.|.	.|.	ENSG00000147206|ENSG00000147206	ENST00000427570|ENST00000395065;ENST00000425463	.|T;T	.|0.33865	.|1.39;1.39	3.64|3.64	1.2|1.2	0.21068|0.21068	.|.	.|0.308479	.|0.33364	.|N	.|0.004994	T|T	0.07638|0.07638	0.0192|0.0192	N|N	0.00686|0.00686	-1.255|-1.255	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.17852	.|0.024;0.011;0.004	.|B;B;B	.|0.10450	.|0.005;0.003;0.001	T|T	0.37314|0.37314	-0.9711|-0.9711	5|10	.|0.02654	.|T	.|1	-12.7344|-12.7344	4.8575|4.8575	0.13566|0.13566	0.0:0.2749:0.0:0.7251|0.0:0.2749:0.0:0.7251	.|.	.|253;149;253	.|B4DYI1;E9PEY7;Q9H4D5	.|.;.;NXF3_HUMAN	H|I	129|253;164	.|ENSP00000378504:V253I;ENSP00000404347:V164I	.|ENSP00000378504:V253I	R|V	-|-	2|1	0|0	NXF3|NXF3	102224367|102224367	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.923000|0.923000	0.28757|0.28757	0.139000|0.139000	0.18822|0.18822	-0.881000|-0.881000	0.02953|0.02953	CGT|GTC	.		0.478	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052	
DOCK11	139818	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	117731503	117731503	+	Silent	SNP	A	A	T			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chrX:117731503A>T	ENST00000276202.7	+	21	2436	c.2373A>T	c.(2371-2373)gcA>gcT	p.A791A	DOCK11_ENST00000276204.6_Silent_p.A791A	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	791	DHR-1.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TGAATGATGCAGAATCAAGAA	0.398																																					p.A791A		.											.	DOCK11-93	0			c.A2373T						.						92.0	82.0	85.0					X																	117731503		2203	4300	6503	SO:0001819	synonymous_variant	139818	exon21			TGATGCAGAATCA	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"""Pleckstrin homology (PH) domain containing"""	23483	protein-coding gene	gene with protein product	"""zizimin2"""	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.2373A>T	X.37:g.117731503A>T		Somatic	90	0		WXS	Illumina HiSeq	Phase_I	91	87	NM_144658	0	0	0	0	0	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																			.		0.398	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
KIAA1210	57481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	118223094	118223094	+	Missense_Mutation	SNP	A	A	G			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chrX:118223094A>G	ENST00000402510.2	-	11	2098	c.2099T>C	c.(2098-2100)aTc>aCc	p.I700T		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	700										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						TTCTAACTGGATATGAGAAGG	0.443																																					p.I700T		.											.	KIAA1210-67	0			c.T2099C						.						46.0	44.0	45.0					X																	118223094		1917	4125	6042	SO:0001583	missense	57481	exon11			AACTGGATATGAG	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.2099T>C	X.37:g.118223094A>G	ENSP00000384670:p.Ile700Thr	Somatic	57	0		WXS	Illumina HiSeq	Phase_I	58	50	NM_020721	0	0	0	0	0	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	37	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	A	12.44	1.939623	0.34189	.	.	ENSG00000250423	ENST00000402510	T	0.15952	2.38	4.42	-4.42	0.03579	.	.	.	.	.	T	0.07007	0.0178	N	0.24115	0.695	0.09310	N	1	B	0.28850	0.225	B	0.29176	0.099	T	0.40021	-0.9585	9	0.12103	T	0.63	.	0.4269	0.00465	0.264:0.1592:0.2924:0.2844	.	700	Q9ULL0	K1210_HUMAN	T	700	ENSP00000384670:I700T	ENSP00000384670:I700T	I	-	2	0	RP13-347D8.6	118107122	0.000000	0.05858	0.000000	0.03702	0.365000	0.29674	-1.161000	0.03144	-1.043000	0.03258	0.350000	0.21858	ATC	.		0.443	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721	
PLXNA3	55558	ucsc.edu	37	X	153696321	153696321	+	Missense_Mutation	SNP	G	G	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chrX:153696321G>A	ENST00000369682.3	+	21	3972	c.3797G>A	c.(3796-3798)cGt>cAt	p.R1266H		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1266					axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTGGAGTCCCGTGTGGCCCTG	0.652																																					p.R1266H													.	PLXNA3-132	0			c.G3797A						.						69.0	62.0	64.0					X																	153696321		2203	4300	6503	SO:0001583	missense	55558	exon21			AGTCCCGTGTGGC	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.3797G>A	X.37:g.153696321G>A	ENSP00000358696:p.Arg1266His	Somatic	75	0		WXS	Illumina HiSeq		33	4	NM_017514	0	0	11	11	0	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812722	0.70912	.	.	ENSG00000130827	ENST00000369682	T	0.01051	5.4	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.06872	0.0175	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.04268	-1.0964	10	0.87932	D	0	.	15.5445	0.76086	0.0:0.0:1.0:0.0	.	1266	P51805	PLXA3_HUMAN	H	1266	ENSP00000358696:R1266H	ENSP00000358696:R1266H	R	+	2	0	PLXNA3	153349515	1.000000	0.71417	0.996000	0.52242	0.457000	0.32468	9.508000	0.98000	1.998000	0.58463	0.436000	0.28706	CGT	.		0.652	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
KRT76	51350	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	12	53170736	53170736	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:53170736delT	ENST00000332411.2	-	1	393	c.340delA	c.(340-342)agtfs	p.S114fs		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	114	Head.				cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						ccaaaaccactacctactcct	0.607																																					p.S114fs		.											.	KRT76-154	0			c.340delA						.						268.0	276.0	273.0					12																	53170736		2203	4299	6502	SO:0001589	frameshift_variant	51350	exon1			.	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.340delA	12.37:g.53170736delT	ENSP00000330101:p.Ser114fs	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	54	24	NM_015848	0	0	0	0	0	B4DRR3|Q7Z795	Frame_Shift_Del	DEL	ENST00000332411.2	37	CCDS8838.1																																																																																			.		0.607	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
GABRG3	2567	hgsc.bcm.edu	37	15	27777872	27777876	+	Frame_Shift_Del	DEL	TTCTT	TTCTT	-			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	TTCTT	TTCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr15:27777872_27777876delTTCTT	ENST00000333743.6	+	10	1503_1507	c.1249_1253delTTCTT	c.(1249-1254)ttcttcfs	p.FF417fs	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	417					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTGTCAGAGCTTCTTCTGCTGCTAT	0.463																																					p.417_418del	NSCLC(114;800 1656 7410 37729 45293)	.											.	.	0			c.1249_1253del						.																																			SO:0001589	frameshift_variant	2567	exon10			.		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.1249_1253delTTCTT	15.37:g.27777872_27777876delTTCTT	ENSP00000331912:p.Phe417fs	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	42	14	NM_033223	0	0	0	0	0	G3V594|Q9HD46|Q9NYT2	Frame_Shift_Del	DEL	ENST00000333743.6	37	CCDS45195.1																																																																																			.		0.463	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
PSME4	23198	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	54147352	54147352	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:54147352delC	ENST00000404125.1	-	19	2453	c.2398delG	c.(2398-2400)gatfs	p.D800fs	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	800					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			AGTTTTCCATCCCCACAATGC	0.383																																					p.D800fs		.											.	PSME4-275	0			c.2398delG						.						149.0	171.0	164.0					2																	54147352		2203	4300	6503	SO:0001589	frameshift_variant	23198	exon19			.	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.2398delG	2.37:g.54147352delC	ENSP00000384211:p.Asp800fs	Somatic	456	0		WXS	Illumina HiSeq	Phase_I	468	189	NM_014614	0	0	0	0	0	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Frame_Shift_Del	DEL	ENST00000404125.1	37	CCDS33197.2																																																																																			.		0.383	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
COL6A6	131873	hgsc.bcm.edu;bcgsc.ca	37	3	130311918	130311918	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:130311918delA	ENST00000358511.6	+	15	4416	c.4385delA	c.(4384-4386)gaafs	p.E1462fs	COL6A6_ENST00000453409.2_Frame_Shift_Del_p.E1462fs	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1462	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GAAGTTGGGGAAAATGGAATT	0.368																																					p.E1462fs		.											.	COL6A6-76	0			c.4385delA						.						270.0	259.0	262.0					3																	130311918		1862	4097	5959	SO:0001589	frameshift_variant	131873	exon15			.	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.4385delA	3.37:g.130311918delA	ENSP00000351310:p.Glu1462fs	Somatic	413	0		WXS	Illumina HiSeq	Phase_I	395	66	NM_001102608	0	0	0	0	0	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Frame_Shift_Del	DEL	ENST00000358511.6	37	CCDS46911.1																																																																																			.		0.368	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
RGS7BP	401190	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	63905047	63905047	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr5:63905047delT	ENST00000334025.2	+	6	1068	c.742delT	c.(742-744)ttcfs	p.F249fs		NM_001029875.1|NM_001271890.1|NM_001271891.1	NP_001025046.1|NP_001258819.1|NP_001258820.1	Q6MZT1	R7BP_HUMAN	regulator of G-protein signaling 7 binding protein	249					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|stomach(1)	11		Lung NSC(810;0.000518)|Prostate(74;0.0435)|Ovarian(174;0.186)		Lung(70;0.147)		GAAGAGAAGGTTCTTTGGGCT	0.478																																					p.F248fs		.											.	RGS7BP-68	0			c.742delT						.						168.0	148.0	155.0					5																	63905047		2203	4300	6503	SO:0001589	frameshift_variant	401190	exon6			.	BX640900	CCDS34170.1	5q12.3	2008-02-05	2007-08-14		ENSG00000186479	ENSG00000186479			23271	protein-coding gene	gene with protein product		610890	"""regulator of G-protein signalling 7 binding protein"""			15632198	Standard	NM_001271890		Approved	R7BP	uc003jtj.4	Q6MZT1	OTTHUMG00000162293	ENST00000334025.2:c.742delT	5.37:g.63905047delT	ENSP00000334851:p.Phe249fs	Somatic	121	0		WXS	Illumina HiSeq	Phase_I	101	38	NM_001029875	0	0	0	0	0	B7Z3X1	Frame_Shift_Del	DEL	ENST00000334025.2	37	CCDS34170.1																																																																																			.		0.478	RGS7BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368464.1	NM_001029875	
LECT2	3950	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	135276238	135276238	+	5'UTR	DEL	A	A	-			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr5:135276238delA	ENST00000471827.1	-	0	523				FBXL21_ENST00000467490.1_RNA|LECT2_ENST00000522943.1_Intron|FBXL21_ENST00000297158.9_RNA			O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2						chemotaxis (GO:0006935)|negative regulation of Wnt signaling pathway (GO:0030178)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	identical protein binding (GO:0042802)			large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ATCATCAATCAAAATTGAAGA	0.333																																					.		.											.	FBXL21-226	0			.						.						74.0	71.0	72.0					5																	135276238		1851	4093	5944	SO:0001623	5_prime_UTR_variant	26223	.			.	AB007546	CCDS4190.1	5q31.1	2008-05-15			ENSG00000145826	ENSG00000145826			6550	protein-coding gene	gene with protein product		602882				9545637	Standard	NM_002302		Approved	chm-II, chm2	uc003lbe.1	O14960	OTTHUMG00000129146	ENST00000471827.1:c.-289T>-	5.37:g.135276238delA		Somatic	40	0		WXS	Illumina HiSeq	Phase_I	62	19	.	0	0	0	0	0	B2RA90|O14565|Q52M49	Targeted_Region	DEL	ENST00000471827.1	37																																																																																				.		0.333	LECT2-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000342497.1	NM_002302	
PLEKHG1	57480	hgsc.bcm.edu;broad.mit.edu	37	6	151152656	151152656	+	Frame_Shift_Del	DEL	T	T	-	rs803411	byFrequency	TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr6:151152656delT	ENST00000358517.2	+	15	2620	c.2409delT	c.(2407-2409)actfs	p.T803fs	PLEKHG1_ENST00000367328.1_Frame_Shift_Del_p.T803fs			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	803							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		ATCAGGCCACTCCCGATCATG	0.512																																					p.T803fs		.											.	PLEKHG1-92	0			c.2409delT						.						116.0	113.0	114.0					6																	151152656		2203	4300	6503	SO:0001589	frameshift_variant	57480	exon16			.	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.2409delT	6.37:g.151152656delT	ENSP00000351318:p.Thr803fs	Somatic	158	0		WXS	Illumina HiSeq	Phase_I	127	60	NM_001029884	0	0	0	0	0	Q5T1F2	Frame_Shift_Del	DEL	ENST00000358517.2	37	CCDS34552.1																																																																																			.		0.512	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
OPLAH	26873	broad.mit.edu	37	8	145113801	145113801	+	Splice_Site	DEL	T	T	-			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:145113801delT	ENST00000426825.1	-	5	545		c.e5-2		OPLAH_ENST00000534424.1_Splice_Site	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)						glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCGTGCGGCCTTCCAGAAAAG	0.677																																					.													.	OPLAH-68	0			c.464-2A>-						.						9.0	12.0	11.0					8																	145113801		1857	4034	5891	SO:0001630	splice_region_variant	26873	exon6			GCGGCCTTCCAGA	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.464-2A>-	8.37:g.145113801delT		Somatic	14	0		WXS	Illumina HiSeq	Phase_I	6	2	NM_017570	0	0	0	0	0	A5PKY8|Q75W65|Q9Y4Q0	Splice_Site	DEL	ENST00000426825.1	37																																																																																				.		0.677	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	Intron
BHMT	635	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	78426827	78426828	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr5:78426827_78426828insA	ENST00000274353.5	+	8	1216_1217	c.1109_1110insA	c.(1108-1113)ccagatfs	p.D371fs	BHMT_ENST00000524080.1_Frame_Shift_Ins_p.D218fs|DMGDH_ENST00000520388.1_Intron	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	371					amino-acid betaine catabolic process (GO:0006579)|amino-acid betaine metabolic process (GO:0006577)|cellular nitrogen compound metabolic process (GO:0034641)|L-methionine salvage (GO:0071267)|protein methylation (GO:0006479)|regulation of homocysteine metabolic process (GO:0050666)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	betaine-homocysteine S-methyltransferase activity (GO:0047150)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)	29		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	ATGTCAAAGCCAGATGGCTGGG	0.495																																					p.P370fs		.											.	BHMT-91	0			c.1109_1110insA						.																																			SO:0001589	frameshift_variant	635	exon8			.	BC012616	CCDS4046.1	5q14.1	2012-09-20	2010-04-28		ENSG00000145692	ENSG00000145692	2.1.1.5		1047	protein-coding gene	gene with protein product	"""betaine homocysteine methyltransferase"""	602888				8798461, 9281325	Standard	NM_001713		Approved	BHMT1	uc003kfu.4	Q93088	OTTHUMG00000108157	ENST00000274353.5:c.1110dupA	5.37:g.78426828_78426828dupA	ENSP00000274353:p.Asp371fs	Somatic	276	0		WXS	Illumina HiSeq	Phase_I	276	105	NM_001713	0	0	0	0	0	Q9UNI9	Frame_Shift_Ins	INS	ENST00000274353.5	37	CCDS4046.1																																																																																			.		0.495	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713	
IREB2	3658	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	78765688	78765689	+	Missense_Mutation	DNP	GT	GT	AC	rs371991607		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr15:78765688_78765689GT>AC	ENST00000258886.8	+	8	1137_1138	c.988_989GT>AC	c.(988-990)GTt>ACt	p.V330T	IREB2_ENST00000560440.1_Missense_Mutation_p.V330T	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	330					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		AAACCCTTTTGTTACATCCATA	0.371																																					p.V330T	NSCLC(200;764 2208 35157 49871 50830)	.											.	IREB2	0			c.T989C						.																																			SO:0001583	missense	3658	exon8			CTTTTGTTACATC	M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	Exception_encountered	15.37:g.78765688_78765689delinsAC	ENSP00000258886:p.Val330Thr	Somatic	116.0	1.0		WXS	Illumina HiSeq	Phase_I	108.0	49.0		0	0	0	0	0	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	DNP	ENST00000258886.8	37	CCDS10302.1																																																																																			.		0.371	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136	
ZNF573	126231	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	38230139	38230140	+	Nonsense_Mutation	DNP	CC	CC	AA			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr19:38230139_38230140CC>AA	ENST00000590414.2	-	4	1272_1273	c.1251_1252GG>TT	c.(1249-1254)aaGGaa>aaTTaa	p.417_418KE>N*	ZNF573_ENST00000357309.3_Nonsense_Mutation_p.329_330KE>N*|ZNF573_ENST00000536220.1_Nonsense_Mutation_p.329_330KE>N*|ZNF573_ENST00000339503.4_Nonsense_Mutation_p.359_360KE>N*|ZNF573_ENST00000392138.1_Nonsense_Mutation_p.330_331KE>N*			Q86YE8	ZN573_HUMAN	zinc finger protein 573	417					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			TTTCCGCATTCCTTGCATTCAT	0.376																																					p.KE359N*		.											.	ZNF573	0			c.G1251T						.																																			SO:0001587	stop_gained	126231	exon5			GCATTCCTTGCAT	AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"""Zinc fingers, C2H2-type"", ""-"""	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.1251_1252delinsAA	19.37:g.38230139_38230140delinsAA	ENSP00000465020:p.K417_E418delinsN*	Somatic	274.0	0.0		WXS	Illumina HiSeq	Phase_I	296.0	132.0		0	0	0	0	0	B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Nonsense_Mutation	DNP	ENST00000590414.2	37	CCDS59381.1																																																																																			.		0.376	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459773.2	NM_152360	
